Starting phenix.real_space_refine on Sat May 17 02:52:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vl5_21230/05_2025/6vl5_21230.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vl5_21230/05_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_21230/05_2025/6vl5_21230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vl5_21230/05_2025/6vl5_21230.map" model { file = "/net/cci-nas-00/data/ceres_data/6vl5_21230/05_2025/6vl5_21230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vl5_21230/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.15, per 1000 atoms: 0.61 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: 4.64 Conformation dependent library (CDL) restraints added in 1.6 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: 2.39 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: 5.66 Time building geometry restraints manager: 5.28 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: 0.620 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: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 36.360 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.390 ------------------------------------------------------------------------------- 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 : 0.394 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: 0.1405 time to fit residues: 20.2633 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 : 0.411 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 : 0.113 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: 0.1545 time to fit residues: 11.6812 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 : 0.125 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: 0.0043 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: 0.0021 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=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 = 0.073202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.061197 restraints weight = 14042.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.063279 restraints weight = 8075.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.064754 restraints weight = 5369.956| |-----------------------------------------------------------------------------| r_work (final): 0.3043 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.079958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.065872 restraints weight = 4500.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.067672 restraints weight = 2576.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.068917 restraints weight = 1729.581| |-----------------------------------------------------------------------------| r_work (final): 0.3118 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.056606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.050705 restraints weight = 290.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.051751 restraints weight = 101.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.051774 restraints weight = 63.531| |-----------------------------------------------------------------------------| r_work (final): 0.2696 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2226 r_free = 0.2226 target = 0.037166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2235 r_free = 0.2235 target = 0.036909 restraints weight = 147.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2227 r_free = 0.2227 target = 0.037043 restraints weight = 14.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2226 r_free = 0.2226 target = 0.037131 restraints weight = 3.063 | |-----------------------------------------------------------------------------| r_work (final): 0.2226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.123 15453 Z= 0.364 Angle : 1.297 31.000 21174 Z= 0.623 Chirality : 0.059 0.310 2658 Planarity : 0.009 0.196 2499 Dihedral : 10.106 90.301 4005 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 20.04 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 C 383 TYR 0.025 0.004 TYR A 39 ARG 0.010 0.001 ARG F 588 Details of bonding type rmsd link_NAG-ASN : bond 0.01121 ( 66) link_NAG-ASN : angle 7.17592 ( 198) link_ALPHA1-6 : bond 0.00793 ( 3) link_ALPHA1-6 : angle 2.05120 ( 9) link_BETA1-4 : bond 0.00858 ( 33) link_BETA1-4 : angle 1.93334 ( 99) link_ALPHA1-3 : bond 0.02063 ( 3) link_ALPHA1-3 : angle 1.68932 ( 9) hydrogen bonds : bond 0.09369 ( 555) hydrogen bonds : angle 6.02203 ( 1827) SS BOND : bond 0.01397 ( 33) SS BOND : angle 3.72462 ( 66) covalent geometry : bond 0.00825 (15315) covalent geometry : angle 1.07579 (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 73 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.384 Fit side-chains REVERT: E 86 LEU cc_start: 0.9071 (mm) cc_final: 0.8709 (mm) REVERT: E 96 TRP cc_start: 0.8630 (m-90) cc_final: 0.8334 (m-10) REVERT: E 104 MET cc_start: 0.8823 (mmm) cc_final: 0.8549 (tpp) REVERT: E 127 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8146 (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: 73 average time/residue: 0.1546 time to fit residues: 14.0437 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 : 0.390 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 : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 575 GLN cc_start: 0.8491 (mt0) cc_final: 0.8209 (mt0) REVERT: F 579 ARG cc_start: 0.8130 (mtp180) cc_final: 0.7363 (ptt180) REVERT: F 628 TRP cc_start: 0.7299 (m-10) cc_final: 0.5459 (p-90) REVERT: F 649 SER cc_start: 0.9217 (m) cc_final: 0.8318 (m) REVERT: F 651 ASN cc_start: 0.9096 (t0) cc_final: 0.8830 (t0) REVERT: F 652 GLN cc_start: 0.9114 (mt0) cc_final: 0.8854 (mm-40) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.1309 time to fit residues: 7.2629 Evaluate side-chains 33 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.102 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 : 0.002 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 ************** Weight determination summary: number of chunks: 168 random chunks: chunk 79 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 2 optimal weight: 0.2980 chunk 3 optimal weight: 0.0060 chunk 78 optimal weight: 0.4980 chunk 118 optimal weight: 0.0970 chunk 159 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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... Flipped N/Q/H residues before XYZ refinement: D 540 GLN D 650 GLN Total number of N/Q/H flips: 2 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 = 0.3217 r_free = 0.3217 target = 0.070636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.059442 restraints weight = 14057.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.061230 restraints weight = 8155.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.062732 restraints weight = 5631.329| |-----------------------------------------------------------------------------| r_work (final): 0.3030 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.079979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.064625 restraints weight = 4715.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.066236 restraints weight = 2850.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.067333 restraints weight = 2002.425| |-----------------------------------------------------------------------------| r_work (final): 0.3053 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.061103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.055087 restraints weight = 395.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.055695 restraints weight = 324.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.056084 restraints weight = 283.031| |-----------------------------------------------------------------------------| r_work (final): 0.2726 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2330 r_free = 0.2330 target = 0.040510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2339 r_free = 0.2339 target = 0.040183 restraints weight = 142.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2330 r_free = 0.2330 target = 0.040409 restraints weight = 17.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2329 r_free = 0.2329 target = 0.040504 restraints weight = 3.481 | |-----------------------------------------------------------------------------| r_work (final): 0.2331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.122 15453 Z= 0.340 Angle : 1.272 30.060 21174 Z= 0.622 Chirality : 0.061 0.412 2658 Planarity : 0.007 0.046 2499 Dihedral : 10.016 87.076 4005 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.39 % Allowed : 2.74 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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 (0.19), residues: 1683 helix: -0.02 (0.24), residues: 390 sheet: 0.16 (0.22), residues: 468 loop : -0.35 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.006 TRP A 112 HIS 0.013 0.003 HIS C 66 PHE 0.022 0.003 PHE B 522 TYR 0.032 0.004 TYR E 40 ARG 0.016 0.001 ARG A 166 Details of bonding type rmsd link_NAG-ASN : bond 0.01045 ( 66) link_NAG-ASN : angle 6.58393 ( 198) link_ALPHA1-6 : bond 0.00352 ( 3) link_ALPHA1-6 : angle 1.85982 ( 9) link_BETA1-4 : bond 0.00459 ( 33) link_BETA1-4 : angle 1.68197 ( 99) link_ALPHA1-3 : bond 0.01198 ( 3) link_ALPHA1-3 : angle 0.84560 ( 9) hydrogen bonds : bond 0.08684 ( 555) hydrogen bonds : angle 6.06100 ( 1827) SS BOND : bond 0.01189 ( 33) SS BOND : angle 2.88642 ( 66) covalent geometry : bond 0.00805 (15315) covalent geometry : angle 1.09259 (20793) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 39 TYR cc_start: 0.8024 (m-10) cc_final: 0.7655 (m-80) REVERT: A 40 TYR cc_start: 0.8517 (t80) cc_final: 0.7885 (p90) REVERT: A 86 LEU cc_start: 0.9148 (mm) cc_final: 0.8904 (mm) REVERT: A 95 MET cc_start: 0.8555 (ppp) cc_final: 0.8298 (ppp) REVERT: A 104 MET cc_start: 0.8851 (mmm) cc_final: 0.8495 (mmm) REVERT: A 288 LEU cc_start: 0.9237 (mt) cc_final: 0.8952 (mp) REVERT: A 308 ARG cc_start: 0.8240 (ttm110) cc_final: 0.7769 (ttt180) REVERT: A 384 TYR cc_start: 0.9194 (m-80) cc_final: 0.8979 (m-10) outliers start: 2 outliers final: 0 residues processed: 70 average time/residue: 0.1359 time to fit residues: 12.1591 Evaluate side-chains 49 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.388 Evaluate side-chains 46 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 543 ASN cc_start: 0.8250 (t0) cc_final: 0.7898 (t0) REVERT: D 575 GLN cc_start: 0.8507 (mt0) cc_final: 0.8098 (mt0) REVERT: D 589 ASP cc_start: 0.8908 (m-30) cc_final: 0.8502 (m-30) REVERT: D 628 TRP cc_start: 0.7236 (m-10) cc_final: 0.5155 (p-90) REVERT: D 633 LYS cc_start: 0.9381 (mtpp) cc_final: 0.9153 (mtmm) REVERT: D 652 GLN cc_start: 0.9300 (mt0) cc_final: 0.8940 (mm-40) REVERT: D 659 ASP cc_start: 0.7813 (m-30) cc_final: 0.7534 (m-30) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1096 time to fit residues: 5.6013 Evaluate side-chains 31 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.122 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: 0.0041 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: 0.0022 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 80 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 125 optimal weight: 0.0020 chunk 26 optimal weight: 7.9990 chunk 55 optimal weight: 0.4980 chunk 130 optimal weight: 0.0030 chunk 77 optimal weight: 0.1980 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 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 = 0.3224 r_free = 0.3224 target = 0.072161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.061062 restraints weight = 14371.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.063086 restraints weight = 8204.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.064548 restraints weight = 5378.454| |-----------------------------------------------------------------------------| r_work (final): 0.3037 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.078775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.064940 restraints weight = 4589.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.066593 restraints weight = 2635.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.067713 restraints weight = 1770.948| |-----------------------------------------------------------------------------| r_work (final): 0.3074 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.061280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.054828 restraints weight = 447.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.055598 restraints weight = 353.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.055888 restraints weight = 301.417| |-----------------------------------------------------------------------------| r_work (final): 0.2730 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2123 r_free = 0.2123 target = 0.033952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2135 r_free = 0.2135 target = 0.033707 restraints weight = 158.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2124 r_free = 0.2124 target = 0.033860 restraints weight = 13.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2123 r_free = 0.2123 target = 0.033942 restraints weight = 2.560 | |-----------------------------------------------------------------------------| r_work (final): 0.2123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.270 15453 Z= 0.439 Angle : 1.329 29.306 21174 Z= 0.646 Chirality : 0.063 0.468 2658 Planarity : 0.008 0.081 2499 Dihedral : 9.887 85.703 4005 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 25.20 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.92 % Favored : 95.72 % Rotamer: Outliers : 0.59 % Allowed : 2.74 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.55 % 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: -0.56 (0.19), residues: 1683 helix: -0.41 (0.24), residues: 393 sheet: 0.06 (0.22), residues: 468 loop : -0.48 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.009 TRP F 610 HIS 0.008 0.002 HIS C 72 PHE 0.016 0.002 PHE F 522 TYR 0.023 0.004 TYR E 39 ARG 0.009 0.001 ARG A 166 Details of bonding type rmsd link_NAG-ASN : bond 0.01535 ( 66) link_NAG-ASN : angle 6.67758 ( 198) link_ALPHA1-6 : bond 0.00832 ( 3) link_ALPHA1-6 : angle 1.88539 ( 9) link_BETA1-4 : bond 0.00605 ( 33) link_BETA1-4 : angle 1.55903 ( 99) link_ALPHA1-3 : bond 0.01401 ( 3) link_ALPHA1-3 : angle 1.53988 ( 9) hydrogen bonds : bond 0.08650 ( 555) hydrogen bonds : angle 6.02790 ( 1827) SS BOND : bond 0.00481 ( 33) SS BOND : angle 2.53759 ( 66) covalent geometry : bond 0.00991 (15315) covalent geometry : angle 1.15785 (20793) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: C 40 TYR cc_start: 0.8632 (t80) cc_final: 0.7747 (p90) REVERT: C 86 LEU cc_start: 0.9158 (mm) cc_final: 0.8899 (mm) REVERT: C 104 MET cc_start: 0.9009 (mmm) cc_final: 0.8804 (tpp) REVERT: C 308 ARG cc_start: 0.8419 (ttm110) cc_final: 0.8006 (ttt180) REVERT: C 384 TYR cc_start: 0.9182 (m-80) cc_final: 0.8955 (m-10) outliers start: 2 outliers final: 1 residues processed: 64 average time/residue: 0.1359 time to fit residues: 11.2268 Evaluate side-chains 42 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.392 Evaluate side-chains 40 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 543 ASN cc_start: 0.8224 (t0) cc_final: 0.7930 (t0) REVERT: D 589 ASP cc_start: 0.8924 (m-30) cc_final: 0.8523 (m-30) REVERT: D 622 ILE cc_start: 0.8284 (mt) cc_final: 0.7780 (mt) REVERT: D 628 TRP cc_start: 0.7298 (m-10) cc_final: 0.5330 (p-90) REVERT: D 633 LYS cc_start: 0.9390 (mtpp) cc_final: 0.9141 (mtmm) REVERT: D 652 GLN cc_start: 0.9264 (mt0) cc_final: 0.8935 (mm-40) REVERT: D 659 ASP cc_start: 0.7771 (m-30) cc_final: 0.7496 (m-30) outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 0.1016 time to fit residues: 4.5685 Evaluate side-chains 30 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.104 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: 0.0035 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 21 optimal weight: 0.0870 chunk 66 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 138 optimal weight: 0.0770 chunk 4 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 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 = 0.3193 r_free = 0.3193 target = 0.069847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.058669 restraints weight = 14715.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.060644 restraints weight = 8273.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.062037 restraints weight = 5436.395| |-----------------------------------------------------------------------------| r_work (final): 0.3007 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.078500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.063926 restraints weight = 4594.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.065464 restraints weight = 2910.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.066559 restraints weight = 2102.184| |-----------------------------------------------------------------------------| r_work (final): 0.3041 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.061146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.054650 restraints weight = 475.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.055264 restraints weight = 364.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.055801 restraints weight = 317.092| |-----------------------------------------------------------------------------| r_work (final): 0.2735 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2250 r_free = 0.2250 target = 0.036726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2252 r_free = 0.2252 target = 0.036499 restraints weight = 164.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2251 r_free = 0.2251 target = 0.036658 restraints weight = 10.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2251 r_free = 0.2251 target = 0.036717 restraints weight = 1.762 | |-----------------------------------------------------------------------------| r_work (final): 0.2250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.142 15453 Z= 0.356 Angle : 1.306 28.489 21174 Z= 0.615 Chirality : 0.064 0.839 2658 Planarity : 0.007 0.066 2499 Dihedral : 10.133 84.634 4005 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.10 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.67 (0.19), residues: 1683 helix: -0.32 (0.25), residues: 372 sheet: -0.00 (0.22), residues: 471 loop : -0.66 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.152 0.009 TRP A 112 HIS 0.052 0.005 HIS A 66 PHE 0.017 0.002 PHE B 522 TYR 0.030 0.003 TYR C 39 ARG 0.016 0.001 ARG E 166 Details of bonding type rmsd link_NAG-ASN : bond 0.01319 ( 66) link_NAG-ASN : angle 6.33071 ( 198) link_ALPHA1-6 : bond 0.00668 ( 3) link_ALPHA1-6 : angle 1.67153 ( 9) link_BETA1-4 : bond 0.00516 ( 33) link_BETA1-4 : angle 1.71032 ( 99) link_ALPHA1-3 : bond 0.01484 ( 3) link_ALPHA1-3 : angle 1.84051 ( 9) hydrogen bonds : bond 0.08029 ( 555) hydrogen bonds : angle 5.95866 ( 1827) SS BOND : bond 0.00464 ( 33) SS BOND : angle 2.44676 ( 66) covalent geometry : bond 0.00846 (15315) covalent geometry : angle 1.14926 (20793) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.426 Fit side-chains REVERT: A 39 TYR cc_start: 0.8237 (m-80) cc_final: 0.7570 (m-80) REVERT: A 40 TYR cc_start: 0.8716 (t80) cc_final: 0.7785 (p90) REVERT: A 86 LEU cc_start: 0.9203 (mm) cc_final: 0.8954 (mm) REVERT: A 95 MET cc_start: 0.8723 (ppp) cc_final: 0.8027 (ppp) REVERT: A 100 MET cc_start: 0.9222 (mtm) cc_final: 0.9018 (mtm) REVERT: A 104 MET cc_start: 0.8961 (mmm) cc_final: 0.8615 (tpp) REVERT: A 308 ARG cc_start: 0.8225 (ttm110) cc_final: 0.7913 (ttt180) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1494 time to fit residues: 11.5831 Evaluate side-chains 44 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.411 Evaluate side-chains 35 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 589 ASP cc_start: 0.8808 (m-30) cc_final: 0.8401 (m-30) REVERT: D 622 ILE cc_start: 0.8567 (mt) cc_final: 0.8169 (mm) REVERT: D 628 TRP cc_start: 0.7213 (m-10) cc_final: 0.5355 (p-90) REVERT: D 633 LYS cc_start: 0.9375 (mtpp) cc_final: 0.9143 (mtmm) REVERT: D 652 GLN cc_start: 0.9211 (mt0) cc_final: 0.8895 (mm-40) REVERT: D 659 ASP cc_start: 0.7744 (m-30) cc_final: 0.7472 (m-30) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0928 time to fit residues: 3.7325 Evaluate side-chains 29 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.106 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 64 optimal weight: 0.0270 chunk 38 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 16 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 overall best weight: 1.6642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3201 r_free = 0.3201 target = 0.070892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.059674 restraints weight = 14454.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.061711 restraints weight = 8059.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.063172 restraints weight = 5255.344| |-----------------------------------------------------------------------------| r_work (final): 0.3010 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.077528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.063823 restraints weight = 4608.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.065403 restraints weight = 2809.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.066410 restraints weight = 1959.275| |-----------------------------------------------------------------------------| r_work (final): 0.3055 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.061077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.054542 restraints weight = 509.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.055169 restraints weight = 367.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.055781 restraints weight = 315.217| |-----------------------------------------------------------------------------| r_work (final): 0.2730 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2122 r_free = 0.2122 target = 0.033625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2136 r_free = 0.2136 target = 0.033394 restraints weight = 177.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2124 r_free = 0.2124 target = 0.033526 restraints weight = 17.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2122 r_free = 0.2122 target = 0.033592 restraints weight = 3.819 | |-----------------------------------------------------------------------------| r_work (final): 0.2140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.170 15453 Z= 0.420 Angle : 1.324 28.135 21174 Z= 0.631 Chirality : 0.057 0.290 2658 Planarity : 0.007 0.071 2499 Dihedral : 10.111 84.115 4005 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 24.40 Ramachandran Plot: Outliers : 0.53 % Allowed : 3.92 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.75 (0.19), residues: 1683 helix: -0.44 (0.26), residues: 372 sheet: -0.05 (0.22), residues: 471 loop : -0.68 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.007 TRP E 96 HIS 0.019 0.003 HIS E 66 PHE 0.014 0.002 PHE B 522 TYR 0.017 0.003 TYR D 638 ARG 0.005 0.001 ARG E 166 Details of bonding type rmsd link_NAG-ASN : bond 0.03420 ( 66) link_NAG-ASN : angle 7.04750 ( 198) link_ALPHA1-6 : bond 0.00574 ( 3) link_ALPHA1-6 : angle 1.66053 ( 9) link_BETA1-4 : bond 0.00457 ( 33) link_BETA1-4 : angle 1.61109 ( 99) link_ALPHA1-3 : bond 0.01385 ( 3) link_ALPHA1-3 : angle 1.75081 ( 9) hydrogen bonds : bond 0.08036 ( 555) hydrogen bonds : angle 5.97605 ( 1827) SS BOND : bond 0.00919 ( 33) SS BOND : angle 2.74261 ( 66) covalent geometry : bond 0.00934 (15315) covalent geometry : angle 1.12831 (20793) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: C 40 TYR cc_start: 0.8577 (t80) cc_final: 0.7768 (p90) REVERT: C 86 LEU cc_start: 0.9186 (mm) cc_final: 0.8873 (mm) REVERT: C 95 MET cc_start: 0.8740 (ppp) cc_final: 0.8219 (ppp) REVERT: C 308 ARG cc_start: 0.8410 (ttm110) cc_final: 0.8078 (ttt180) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1302 time to fit residues: 9.7017 Evaluate side-chains 43 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.391 Evaluate side-chains 36 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 530 MET cc_start: 0.8341 (mtm) cc_final: 0.8036 (mtt) REVERT: D 589 ASP cc_start: 0.8832 (m-30) cc_final: 0.8412 (m-30) REVERT: D 622 ILE cc_start: 0.8540 (mt) cc_final: 0.8281 (mm) REVERT: D 628 TRP cc_start: 0.7291 (m-10) cc_final: 0.5351 (p-90) REVERT: D 633 LYS cc_start: 0.9379 (mtpp) cc_final: 0.9138 (mtmm) REVERT: D 652 GLN cc_start: 0.9231 (mt0) cc_final: 0.8898 (mm-40) REVERT: D 659 ASP cc_start: 0.7764 (m-30) cc_final: 0.7482 (m-30) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0863 time to fit residues: 3.5637 Evaluate side-chains 30 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.148 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: 0.0043 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: 0.0020 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 67 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 83 optimal weight: 0.1980 chunk 166 optimal weight: 0.4980 chunk 33 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 159 optimal weight: 0.0670 chunk 9 optimal weight: 0.0870 chunk 47 optimal weight: 0.0670 chunk 154 optimal weight: 2.9990 overall best weight: 0.1834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3228 r_free = 0.3228 target = 0.072425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.061139 restraints weight = 14357.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.063190 restraints weight = 8103.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.064664 restraints weight = 5321.344| |-----------------------------------------------------------------------------| r_work (final): 0.3045 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.078158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.063726 restraints weight = 4783.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.065279 restraints weight = 2904.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.066422 restraints weight = 2054.592| |-----------------------------------------------------------------------------| r_work (final): 0.3038 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.061290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.054960 restraints weight = 458.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.055686 restraints weight = 351.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.056184 restraints weight = 297.318| |-----------------------------------------------------------------------------| r_work (final): 0.2736 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2155 r_free = 0.2155 target = 0.034200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 19)----------------| | r_work = 0.2157 r_free = 0.2157 target = 0.033895 restraints weight = 165.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2155 r_free = 0.2155 target = 0.034089 restraints weight = 16.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2155 r_free = 0.2155 target = 0.034188 restraints weight = 3.677 | |-----------------------------------------------------------------------------| r_work (final): 0.2168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.239 15453 Z= 0.433 Angle : 1.447 37.954 21174 Z= 0.668 Chirality : 0.065 0.568 2658 Planarity : 0.007 0.081 2499 Dihedral : 10.133 83.089 4005 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 24.02 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.28 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.55 % 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: -0.94 (0.20), residues: 1683 helix: -0.73 (0.24), residues: 390 sheet: -0.11 (0.22), residues: 471 loop : -0.77 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.098 0.009 TRP C 112 HIS 0.012 0.003 HIS A 66 PHE 0.016 0.002 PHE F 522 TYR 0.028 0.003 TYR A 217 ARG 0.006 0.000 ARG B 588 Details of bonding type rmsd link_NAG-ASN : bond 0.02652 ( 66) link_NAG-ASN : angle 6.54332 ( 198) link_ALPHA1-6 : bond 0.00602 ( 3) link_ALPHA1-6 : angle 1.72827 ( 9) link_BETA1-4 : bond 0.00554 ( 33) link_BETA1-4 : angle 1.61234 ( 99) link_ALPHA1-3 : bond 0.01192 ( 3) link_ALPHA1-3 : angle 1.63279 ( 9) hydrogen bonds : bond 0.08984 ( 555) hydrogen bonds : angle 6.03694 ( 1827) SS BOND : bond 0.00405 ( 33) SS BOND : angle 2.74851 ( 66) covalent geometry : bond 0.00965 (15315) covalent geometry : angle 1.29780 (20793) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.427 Fit side-chains REVERT: C 40 TYR cc_start: 0.8514 (t80) cc_final: 0.7782 (p90) REVERT: C 86 LEU cc_start: 0.9214 (mm) cc_final: 0.8920 (mm) REVERT: C 308 ARG cc_start: 0.8386 (ttm110) cc_final: 0.7901 (ttt180) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1477 time to fit residues: 10.3605 Evaluate side-chains 44 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.425 Evaluate side-chains 37 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 530 MET cc_start: 0.8393 (mtm) cc_final: 0.8152 (mtt) REVERT: D 589 ASP cc_start: 0.8903 (m-30) cc_final: 0.8486 (m-30) REVERT: D 622 ILE cc_start: 0.8426 (mt) cc_final: 0.8056 (mm) REVERT: D 628 TRP cc_start: 0.7266 (m-10) cc_final: 0.5383 (p-90) REVERT: D 633 LYS cc_start: 0.9414 (mtpp) cc_final: 0.9172 (mtmm) REVERT: D 652 GLN cc_start: 0.9288 (mt0) cc_final: 0.8929 (mm-40) REVERT: D 659 ASP cc_start: 0.7891 (m-30) cc_final: 0.7563 (m-30) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0964 time to fit residues: 4.1380 Evaluate side-chains 29 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.118 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: 0.0041 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: 0.0022 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 136 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 165 optimal weight: 0.0060 chunk 1 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 49 optimal weight: 30.0000 chunk 161 optimal weight: 30.0000 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3224 r_free = 0.3224 target = 0.071648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.060252 restraints weight = 14746.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.062271 restraints weight = 8252.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.063698 restraints weight = 5407.646| |-----------------------------------------------------------------------------| r_work (final): 0.3029 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.078244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.063821 restraints weight = 4872.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.065364 restraints weight = 2962.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.066500 restraints weight = 2099.809| |-----------------------------------------------------------------------------| r_work (final): 0.3039 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.061348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.054807 restraints weight = 509.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.055394 restraints weight = 370.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.056102 restraints weight = 318.856| |-----------------------------------------------------------------------------| r_work (final): 0.2737 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.071565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.069841 restraints weight = 104.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.070182 restraints weight = 10.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.070240 restraints weight = 1.562 | |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.227 15453 Z= 0.438 Angle : 1.459 30.701 21174 Z= 0.668 Chirality : 0.061 0.374 2658 Planarity : 0.007 0.090 2499 Dihedral : 10.009 82.597 4005 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 25.71 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.28 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.55 % 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: -0.98 (0.19), residues: 1683 helix: -0.78 (0.24), residues: 390 sheet: -0.16 (0.22), residues: 471 loop : -0.76 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.105 0.009 TRP D 610 HIS 0.034 0.004 HIS A 66 PHE 0.014 0.002 PHE F 522 TYR 0.070 0.004 TYR E 39 ARG 0.005 0.001 ARG A 166 Details of bonding type rmsd link_NAG-ASN : bond 0.02078 ( 66) link_NAG-ASN : angle 7.07539 ( 198) link_ALPHA1-6 : bond 0.00589 ( 3) link_ALPHA1-6 : angle 1.70440 ( 9) link_BETA1-4 : bond 0.00609 ( 33) link_BETA1-4 : angle 1.56340 ( 99) link_ALPHA1-3 : bond 0.01037 ( 3) link_ALPHA1-3 : angle 1.68153 ( 9) hydrogen bonds : bond 0.08401 ( 555) hydrogen bonds : angle 5.98465 ( 1827) SS BOND : bond 0.01651 ( 33) SS BOND : angle 2.67649 ( 66) covalent geometry : bond 0.01023 (15315) covalent geometry : angle 1.28669 (20793) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.393 Fit side-chains REVERT: C 40 TYR cc_start: 0.8542 (t80) cc_final: 0.7778 (p90) REVERT: C 86 LEU cc_start: 0.9213 (mm) cc_final: 0.8925 (mm) REVERT: C 155 LYS cc_start: 0.8508 (mmtm) cc_final: 0.8113 (mmmm) REVERT: C 180 ASP cc_start: 0.9113 (m-30) cc_final: 0.8885 (m-30) REVERT: C 308 ARG cc_start: 0.8376 (ttm110) cc_final: 0.7966 (ttt180) REVERT: C 426 MET cc_start: 0.7959 (ptm) cc_final: 0.7494 (ptm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1378 time to fit residues: 9.4929 Evaluate side-chains 42 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.403 Evaluate side-chains 38 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 530 MET cc_start: 0.8375 (mtm) cc_final: 0.8129 (mtt) REVERT: D 589 ASP cc_start: 0.8893 (m-30) cc_final: 0.8534 (m-30) REVERT: D 622 ILE cc_start: 0.8438 (mt) cc_final: 0.8044 (mm) REVERT: D 628 TRP cc_start: 0.7270 (m-10) cc_final: 0.5362 (p-90) REVERT: D 633 LYS cc_start: 0.9413 (mtpp) cc_final: 0.9186 (mtmm) REVERT: D 652 GLN cc_start: 0.9271 (mt0) cc_final: 0.8920 (mm-40) REVERT: D 659 ASP cc_start: 0.7909 (m-30) cc_final: 0.7586 (m-30) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0903 time to fit residues: 3.9744 Evaluate side-chains 29 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.104 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 : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 48 optimal weight: 0.0020 chunk 108 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 96 optimal weight: 0.1980 chunk 138 optimal weight: 0.0000 chunk 44 optimal weight: 10.0000 chunk 157 optimal weight: 0.4980 chunk 56 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 30 optimal weight: 0.0770 overall best weight: 0.1550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3225 r_free = 0.3225 target = 0.071779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.060402 restraints weight = 14689.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.062444 restraints weight = 8162.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.063843 restraints weight = 5327.066| |-----------------------------------------------------------------------------| r_work (final): 0.3030 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.077784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.063775 restraints weight = 4660.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.065242 restraints weight = 2910.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.066277 restraints weight = 2105.896| |-----------------------------------------------------------------------------| r_work (final): 0.3037 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.061371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.055004 restraints weight = 463.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.055509 restraints weight = 354.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.056107 restraints weight = 311.854| |-----------------------------------------------------------------------------| r_work (final): 0.2738 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2143 r_free = 0.2143 target = 0.034416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.2152 r_free = 0.2152 target = 0.034171 restraints weight = 172.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2143 r_free = 0.2143 target = 0.034329 restraints weight = 14.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2143 r_free = 0.2143 target = 0.034411 restraints weight = 2.596 | |-----------------------------------------------------------------------------| r_work (final): 0.2143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.225 15453 Z= 0.423 Angle : 1.445 35.345 21174 Z= 0.658 Chirality : 0.063 0.537 2658 Planarity : 0.007 0.093 2499 Dihedral : 9.981 82.537 4005 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 26.96 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.28 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.55 % 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: -0.97 (0.19), residues: 1683 helix: -0.75 (0.24), residues: 390 sheet: -0.16 (0.22), residues: 471 loop : -0.77 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.008 TRP D 610 HIS 0.032 0.004 HIS E 66 PHE 0.013 0.002 PHE B 522 TYR 0.048 0.004 TYR E 39 ARG 0.009 0.001 ARG A 166 Details of bonding type rmsd link_NAG-ASN : bond 0.01606 ( 66) link_NAG-ASN : angle 6.91184 ( 198) link_ALPHA1-6 : bond 0.00567 ( 3) link_ALPHA1-6 : angle 1.69164 ( 9) link_BETA1-4 : bond 0.00583 ( 33) link_BETA1-4 : angle 1.54694 ( 99) link_ALPHA1-3 : bond 0.01171 ( 3) link_ALPHA1-3 : angle 1.79026 ( 9) hydrogen bonds : bond 0.08384 ( 555) hydrogen bonds : angle 5.96661 ( 1827) SS BOND : bond 0.01280 ( 33) SS BOND : angle 2.66189 ( 66) covalent geometry : bond 0.01012 (15315) covalent geometry : angle 1.27882 (20793) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.390 Fit side-chains REVERT: C 40 TYR cc_start: 0.8557 (t80) cc_final: 0.7784 (p90) REVERT: C 86 LEU cc_start: 0.9216 (mm) cc_final: 0.8915 (mm) REVERT: C 155 LYS cc_start: 0.8523 (mmtm) cc_final: 0.8108 (mmmm) REVERT: C 308 ARG cc_start: 0.8380 (ttm110) cc_final: 0.7955 (ttt180) REVERT: C 426 MET cc_start: 0.7731 (ptm) cc_final: 0.7522 (ptm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1501 time to fit residues: 10.4262 Evaluate side-chains 43 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.426 Evaluate side-chains 35 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 530 MET cc_start: 0.8398 (mtm) cc_final: 0.8123 (mtt) REVERT: D 589 ASP cc_start: 0.8898 (m-30) cc_final: 0.8538 (m-30) REVERT: D 622 ILE cc_start: 0.8440 (mt) cc_final: 0.8026 (mm) REVERT: D 628 TRP cc_start: 0.7260 (m-10) cc_final: 0.5364 (p-90) REVERT: D 633 LYS cc_start: 0.9407 (mtpp) cc_final: 0.9182 (mtmm) REVERT: D 652 GLN cc_start: 0.9282 (mt0) cc_final: 0.8923 (mm-40) REVERT: D 659 ASP cc_start: 0.7916 (m-30) cc_final: 0.7591 (m-30) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0908 time to fit residues: 3.6530 Evaluate side-chains 28 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.116 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=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 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-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 400, 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 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-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/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-5687/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-5687/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-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: 66.8704 > 50: distance: 0 - 1: 8.179 distance: 0 - 3: 7.484 distance: 1 - 2: 34.055 distance: 1 - 7: 9.997 distance: 3 - 4: 11.317 distance: 4 - 5: 14.521 distance: 4 - 6: 20.200 distance: 7 - 8: 18.496 distance: 8 - 9: 10.047 distance: 8 - 11: 33.407 distance: 9 - 10: 22.395 distance: 9 - 16: 12.135 distance: 11 - 12: 27.826 distance: 12 - 13: 27.145 distance: 13 - 14: 39.189 distance: 14 - 15: 18.704 distance: 16 - 17: 4.505 distance: 16 - 22: 13.443 distance: 17 - 18: 18.757 distance: 17 - 20: 10.059 distance: 18 - 19: 26.297 distance: 18 - 23: 15.320 distance: 20 - 21: 14.029 distance: 21 - 22: 13.702 distance: 23 - 24: 11.268 distance: 24 - 25: 25.714 distance: 24 - 27: 14.868 distance: 25 - 26: 3.148 distance: 25 - 29: 7.749 distance: 27 - 28: 32.267 distance: 29 - 30: 15.779 distance: 30 - 31: 15.487 distance: 30 - 33: 19.486 distance: 31 - 36: 12.685 distance: 33 - 34: 18.571 distance: 33 - 35: 33.673 distance: 36 - 37: 17.884 distance: 37 - 38: 24.422 distance: 37 - 40: 25.786 distance: 38 - 39: 12.762 distance: 38 - 45: 28.049 distance: 40 - 41: 30.280 distance: 41 - 42: 20.984 distance: 42 - 43: 26.011 distance: 43 - 44: 6.329 distance: 45 - 46: 28.921 distance: 46 - 47: 20.588 distance: 46 - 49: 9.161 distance: 47 - 48: 26.077 distance: 47 - 53: 13.764 distance: 48 - 67: 47.044 distance: 49 - 50: 27.882 distance: 50 - 51: 39.548 distance: 50 - 52: 22.084 distance: 53 - 54: 18.132 distance: 54 - 55: 13.847 distance: 54 - 57: 6.922 distance: 55 - 56: 12.700 distance: 55 - 60: 6.397 distance: 56 - 75: 22.739 distance: 57 - 58: 21.860 distance: 57 - 59: 24.334 distance: 60 - 61: 18.384 distance: 60 - 66: 28.771 distance: 61 - 62: 11.232 distance: 61 - 64: 29.869 distance: 62 - 63: 38.165 distance: 62 - 67: 23.001 distance: 64 - 65: 16.781 distance: 65 - 66: 15.401 distance: 67 - 68: 26.377 distance: 68 - 69: 12.358 distance: 68 - 71: 13.310 distance: 69 - 70: 7.600 distance: 69 - 75: 16.494 distance: 71 - 72: 23.189 distance: 72 - 73: 22.910 distance: 72 - 74: 6.341 distance: 75 - 76: 35.759 distance: 76 - 77: 11.719 distance: 76 - 79: 45.057 distance: 77 - 78: 14.431 distance: 77 - 81: 13.459 distance: 79 - 80: 35.556 distance: 81 - 82: 33.501 distance: 82 - 83: 10.740 distance: 82 - 85: 18.854 distance: 83 - 84: 6.880 distance: 83 - 88: 21.670 distance: 85 - 86: 14.332 distance: 85 - 87: 26.487 distance: 88 - 89: 6.848 distance: 89 - 90: 10.661 distance: 89 - 92: 9.779 distance: 90 - 91: 12.488 distance: 92 - 93: 12.909