Starting phenix.real_space_refine on Wed Jun 25 05:37:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6q04_20542/06_2025/6q04_20542.cif Found real_map, /net/cci-nas-00/data/ceres_data/6q04_20542/06_2025/6q04_20542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6q04_20542/06_2025/6q04_20542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6q04_20542/06_2025/6q04_20542.map" model { file = "/net/cci-nas-00/data/ceres_data/6q04_20542/06_2025/6q04_20542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6q04_20542/06_2025/6q04_20542.cif" } resolution = 2.5 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= 0.003 sd= 0.101 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 147 5.16 5 C 18108 2.51 5 N 4533 2.21 5 O 6123 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 165 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28911 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8952 Classifications: {'peptide': 1159} Link IDs: {'PTRANS': 58, 'TRANS': 1100} Chain breaks: 4 Chain: "B" Number of atoms: 8952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8952 Classifications: {'peptide': 1159} Link IDs: {'PTRANS': 58, 'TRANS': 1100} Chain breaks: 4 Chain: "C" Number of atoms: 8952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8952 Classifications: {'peptide': 1159} Link IDs: {'PTRANS': 58, 'TRANS': 1100} Chain breaks: 4 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: "L" 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: "V" 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: "f" 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: "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: "A" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 151 Unusual residues: {'FOL': 1, 'NAG': 7, 'SIA': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 151 Unusual residues: {'FOL': 1, 'NAG': 7, 'SIA': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 151 Unusual residues: {'FOL': 1, 'NAG': 7, 'SIA': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Time building chain proxies: 15.78, per 1000 atoms: 0.55 Number of scatterers: 28911 At special positions: 0 Unit cell: (141.75, 150.15, 160.65, 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 147 16.00 O 6123 8.00 N 4533 7.00 C 18108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.08 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.06 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.01 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.17 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.09 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.02 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.02 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.06 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.03 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.12 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.09 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.04 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.05 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.08 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.06 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.02 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.17 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.09 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.02 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.02 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.06 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.12 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.09 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.04 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.05 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.08 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.06 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.02 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.17 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.09 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.02 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.02 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.06 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.12 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.09 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.04 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.05 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " 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 ALPHA1-2 " MAN F 4 " - " MAN F 5 " " MAN F 6 " - " MAN F 7 " " MAN P 4 " - " MAN P 5 " " MAN P 6 " - " MAN P 7 " " MAN Z 4 " - " MAN Z 5 " " MAN Z 6 " - " MAN Z 7 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 4 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA F 3 " - " MAN F 6 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 5 " " BMA P 3 " - " MAN P 6 " " BMA U 3 " - " MAN U 5 " " BMA V 3 " - " MAN V 5 " " BMA Z 3 " - " MAN Z 6 " " BMA e 3 " - " MAN e 5 " " BMA f 3 " - " MAN f 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A1414 " - " ASN A 487 " " NAG A1415 " - " ASN A 592 " " NAG A1416 " - " ASN A 619 " " NAG A1417 " - " ASN A 719 " " NAG A1418 " - " ASN A 774 " " NAG A1419 " - " ASN A 785 " " NAG A1436 " - " ASN A 155 " " NAG B1414 " - " ASN B 487 " " NAG B1415 " - " ASN B 592 " " NAG B1416 " - " ASN B 619 " " NAG B1417 " - " ASN B 719 " " NAG B1418 " - " ASN B 774 " " NAG B1419 " - " ASN B 785 " " NAG B1436 " - " ASN B 155 " " NAG C1414 " - " ASN C 487 " " NAG C1415 " - " ASN C 592 " " NAG C1416 " - " ASN C 619 " " NAG C1417 " - " ASN C 719 " " NAG C1418 " - " ASN C 774 " " NAG C1419 " - " ASN C 785 " " NAG C1436 " - " ASN C 155 " " NAG D 1 " - " ASN A 222 " " NAG E 1 " - " ASN A 236 " " NAG F 1 " - " ASN A 410 " " NAG G 1 " - " ASN A 870 " " NAG H 1 " - " ASN A1213 " " NAG I 1 " - " ASN A 66 " " NAG J 1 " - " ASN A 104 " " NAG K 1 " - " ASN A 125 " " NAG L 1 " - " ASN A 166 " " NAG M 1 " - " ASN A 244 " " NAG N 1 " - " ASN B 222 " " NAG O 1 " - " ASN B 236 " " NAG P 1 " - " ASN B 410 " " NAG Q 1 " - " ASN B 870 " " NAG R 1 " - " ASN B1213 " " NAG S 1 " - " ASN B 66 " " NAG T 1 " - " ASN B 104 " " NAG U 1 " - " ASN B 125 " " NAG V 1 " - " ASN B 166 " " NAG W 1 " - " ASN B 244 " " NAG X 1 " - " ASN C 222 " " NAG Y 1 " - " ASN C 236 " " NAG Z 1 " - " ASN C 410 " " NAG a 1 " - " ASN C 870 " " NAG b 1 " - " ASN C1213 " " NAG c 1 " - " ASN C 66 " " NAG d 1 " - " ASN C 104 " " NAG e 1 " - " ASN C 125 " " NAG f 1 " - " ASN C 166 " " NAG g 1 " - " ASN C 244 " Time building additional restraints: 8.51 Conformation dependent library (CDL) restraints added in 3.2 seconds 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB FOL A1444 " pdb=" CB FOL B1444 " pdb=" CB FOL C1444 " Number of C-beta restraints generated: 6456 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 57 sheets defined 27.4% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.21 Creating SS restraints... Processing helix chain 'A' and resid 37 through 41 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.854A pdb=" N TYR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 removed outlier: 4.150A pdb=" N ARG A 307 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.774A pdb=" N PHE A 399 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.825A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 434 removed outlier: 4.027A pdb=" N ALA A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 457 removed outlier: 5.380A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 524 through 529 removed outlier: 3.917A pdb=" N SER A 528 " --> pdb=" O PRO A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 596 through 600 removed outlier: 3.837A pdb=" N LEU A 600 " --> pdb=" O ALA A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'A' and resid 678 through 682 Processing helix chain 'A' and resid 805 through 812 Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 823 through 825 No H-bonds generated for 'chain 'A' and resid 823 through 825' Processing helix chain 'A' and resid 826 through 854 removed outlier: 3.792A pdb=" N GLN A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 897 Processing helix chain 'A' and resid 907 through 915 removed outlier: 3.679A pdb=" N MET A 913 " --> pdb=" O TYR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 931 Processing helix chain 'A' and resid 940 through 953 Processing helix chain 'A' and resid 954 through 959 Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1007 Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 4.173A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1107 removed outlier: 4.318A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.853A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 removed outlier: 4.150A pdb=" N ARG B 307 " --> pdb=" O GLN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 385 through 390 Processing helix chain 'B' and resid 395 through 399 removed outlier: 3.773A pdb=" N PHE B 399 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.825A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 434 removed outlier: 4.027A pdb=" N ALA B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 457 removed outlier: 5.380A pdb=" N SER B 454 " --> pdb=" O SER B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 524 through 529 removed outlier: 3.918A pdb=" N SER B 528 " --> pdb=" O PRO B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 596 through 600 removed outlier: 3.836A pdb=" N LEU B 600 " --> pdb=" O ALA B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 628 Processing helix chain 'B' and resid 678 through 682 Processing helix chain 'B' and resid 805 through 812 Processing helix chain 'B' and resid 814 through 822 Processing helix chain 'B' and resid 823 through 825 No H-bonds generated for 'chain 'B' and resid 823 through 825' Processing helix chain 'B' and resid 826 through 854 removed outlier: 3.792A pdb=" N GLN B 842 " --> pdb=" O ALA B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 897 Processing helix chain 'B' and resid 907 through 915 removed outlier: 3.679A pdb=" N MET B 913 " --> pdb=" O TYR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 931 Processing helix chain 'B' and resid 940 through 953 Processing helix chain 'B' and resid 954 through 959 Processing helix chain 'B' and resid 971 through 982 Processing helix chain 'B' and resid 986 through 993 Processing helix chain 'B' and resid 993 through 1007 Processing helix chain 'B' and resid 1016 through 1040 removed outlier: 4.173A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU B1040 " --> pdb=" O LEU B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1058 Processing helix chain 'B' and resid 1059 through 1107 removed outlier: 4.318A pdb=" N ALA B1065 " --> pdb=" O PRO B1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.854A pdb=" N TYR C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 removed outlier: 4.150A pdb=" N ARG C 307 " --> pdb=" O GLN C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 395 through 399 removed outlier: 3.774A pdb=" N PHE C 399 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.825A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 434 removed outlier: 4.028A pdb=" N ALA C 434 " --> pdb=" O PRO C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 457 removed outlier: 5.380A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 524 through 529 removed outlier: 3.918A pdb=" N SER C 528 " --> pdb=" O PRO C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 596 through 600 removed outlier: 3.837A pdb=" N LEU C 600 " --> pdb=" O ALA C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 628 Processing helix chain 'C' and resid 678 through 682 Processing helix chain 'C' and resid 805 through 812 Processing helix chain 'C' and resid 814 through 822 Processing helix chain 'C' and resid 823 through 825 No H-bonds generated for 'chain 'C' and resid 823 through 825' Processing helix chain 'C' and resid 826 through 854 removed outlier: 3.792A pdb=" N GLN C 842 " --> pdb=" O ALA C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 897 Processing helix chain 'C' and resid 907 through 915 removed outlier: 3.680A pdb=" N MET C 913 " --> pdb=" O TYR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 931 Processing helix chain 'C' and resid 940 through 953 Processing helix chain 'C' and resid 954 through 959 Processing helix chain 'C' and resid 971 through 982 Processing helix chain 'C' and resid 986 through 993 Processing helix chain 'C' and resid 993 through 1007 Processing helix chain 'C' and resid 1016 through 1040 removed outlier: 4.174A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU C1040 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1058 Processing helix chain 'C' and resid 1059 through 1107 removed outlier: 4.319A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 removed outlier: 6.599A pdb=" N THR A 63 " --> pdb=" O TYR C 632 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 75 removed outlier: 4.165A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.039A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.167A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.417A pdb=" N LEU A 180 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR A 241 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA A 182 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE A 239 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR A 184 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS A 237 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 127 through 130 removed outlier: 5.424A pdb=" N THR A 136 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 309 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AB1, first strand: chain 'A' and resid 359 through 366 removed outlier: 4.571A pdb=" N VAL A 659 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER A 365 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL A 657 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY A 675 " --> pdb=" O PRO A 658 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 373 through 376 removed outlier: 4.760A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 631 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 400 through 404 removed outlier: 3.524A pdb=" N SER A 440 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL A 420 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 407 through 409 Processing sheet with id=AB5, first strand: chain 'A' and resid 513 through 515 removed outlier: 5.437A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 717 through 724 removed outlier: 6.629A pdb=" N VAL A 718 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N SER A 761 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N SER A 720 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU A 735 " --> pdb=" O LEU A 731 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.469A pdb=" N ILE A 768 " --> pdb=" O SER B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1191 through 1195 removed outlier: 5.656A pdb=" N ALA A1193 " --> pdb=" O GLY A1188 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY A1188 " --> pdb=" O ALA A1193 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS A 779 " --> pdb=" O ALA B 969 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 785 through 796 removed outlier: 5.926A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 801 through 804 removed outlier: 4.610A pdb=" N LYS A 801 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AC3, first strand: chain 'A' and resid 967 through 969 removed outlier: 3.837A pdb=" N LYS C 779 " --> pdb=" O ALA A 969 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N PHE C1172 " --> pdb=" O ALA C1152 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY C1188 " --> pdb=" O ALA C1193 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ALA C1193 " --> pdb=" O GLY C1188 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1202 through 1205 removed outlier: 4.072A pdb=" N CYS A1164 " --> pdb=" O VAL A1205 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AC6, first strand: chain 'B' and resid 67 through 75 removed outlier: 4.166A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.039A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.166A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AD1, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.417A pdb=" N LEU B 180 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR B 241 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA B 182 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE B 239 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR B 184 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS B 237 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 127 through 130 removed outlier: 5.425A pdb=" N THR B 136 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AD4, first strand: chain 'B' and resid 359 through 366 removed outlier: 4.571A pdb=" N VAL B 659 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER B 365 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL B 657 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY B 675 " --> pdb=" O PRO B 658 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 373 through 376 removed outlier: 4.760A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 400 through 404 removed outlier: 3.525A pdb=" N SER B 440 " --> pdb=" O GLN B 576 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 407 through 409 Processing sheet with id=AD8, first strand: chain 'B' and resid 513 through 515 removed outlier: 5.437A pdb=" N SER B 498 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 561 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 717 through 724 removed outlier: 6.629A pdb=" N VAL B 718 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N SER B 761 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N SER B 720 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B 735 " --> pdb=" O LEU B 731 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 768 through 769 removed outlier: 5.469A pdb=" N ILE B 768 " --> pdb=" O SER C 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 1191 through 1195 removed outlier: 5.655A pdb=" N ALA B1193 " --> pdb=" O GLY B1188 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY B1188 " --> pdb=" O ALA B1193 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N PHE B1172 " --> pdb=" O ALA B1152 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS B 779 " --> pdb=" O ALA C 969 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 785 through 796 removed outlier: 5.926A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 801 through 804 removed outlier: 4.610A pdb=" N LYS B 801 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1202 through 1205 removed outlier: 4.072A pdb=" N CYS B1164 " --> pdb=" O VAL B1205 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AE7, first strand: chain 'C' and resid 67 through 75 removed outlier: 4.165A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.039A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.167A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AF2, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.417A pdb=" N LEU C 180 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR C 241 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS C 237 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 127 through 130 removed outlier: 5.424A pdb=" N THR C 136 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AF5, first strand: chain 'C' and resid 359 through 366 removed outlier: 4.571A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER C 365 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL C 657 " --> pdb=" O SER C 365 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY C 675 " --> pdb=" O PRO C 658 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 400 through 404 removed outlier: 3.524A pdb=" N SER C 440 " --> pdb=" O GLN C 576 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 407 through 409 Processing sheet with id=AF8, first strand: chain 'C' and resid 513 through 515 removed outlier: 5.436A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 717 through 724 removed outlier: 6.628A pdb=" N VAL C 718 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N SER C 761 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N SER C 720 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU C 735 " --> pdb=" O LEU C 731 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 785 through 796 removed outlier: 5.926A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 801 through 804 removed outlier: 4.609A pdb=" N LYS C 801 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 4.072A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) 1157 hydrogen bonds defined for protein. 3024 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: 15.67 Time building geometry restraints manager: 9.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.06: 3 1.06 - 1.26: 4510 1.26 - 1.46: 12119 1.46 - 1.66: 12468 1.66 - 1.85: 216 Bond restraints: 29316 Sorted by residual: bond pdb=" C CYS C 383 " pdb=" O CYS C 383 " ideal model delta sigma weight residual 1.234 0.867 0.368 1.22e-02 6.72e+03 9.08e+02 bond pdb=" C CYS A 383 " pdb=" O CYS A 383 " ideal model delta sigma weight residual 1.234 0.867 0.368 1.22e-02 6.72e+03 9.08e+02 bond pdb=" C CYS B 383 " pdb=" O CYS B 383 " ideal model delta sigma weight residual 1.234 0.867 0.367 1.22e-02 6.72e+03 9.05e+02 bond pdb=" C CYS C 383 " pdb=" N ASP C 384 " ideal model delta sigma weight residual 1.331 1.557 -0.226 1.43e-02 4.89e+03 2.49e+02 bond pdb=" C CYS A 383 " pdb=" N ASP A 384 " ideal model delta sigma weight residual 1.331 1.557 -0.226 1.43e-02 4.89e+03 2.49e+02 ... (remaining 29311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 38422 4.37 - 8.74: 1330 8.74 - 13.11: 100 13.11 - 17.48: 21 17.48 - 21.85: 33 Bond angle restraints: 39906 Sorted by residual: angle pdb=" CA CYS C 383 " pdb=" C CYS C 383 " pdb=" O CYS C 383 " ideal model delta sigma weight residual 120.92 142.25 -21.33 1.15e+00 7.56e-01 3.44e+02 angle pdb=" CA CYS A 383 " pdb=" C CYS A 383 " pdb=" O CYS A 383 " ideal model delta sigma weight residual 120.92 142.25 -21.33 1.15e+00 7.56e-01 3.44e+02 angle pdb=" CA CYS B 383 " pdb=" C CYS B 383 " pdb=" O CYS B 383 " ideal model delta sigma weight residual 120.92 142.20 -21.28 1.15e+00 7.56e-01 3.42e+02 angle pdb=" CA CYS B 383 " pdb=" C CYS B 383 " pdb=" N ASP B 384 " ideal model delta sigma weight residual 115.86 94.48 21.38 1.24e+00 6.50e-01 2.97e+02 angle pdb=" CA CYS A 383 " pdb=" C CYS A 383 " pdb=" N ASP A 384 " ideal model delta sigma weight residual 115.86 94.49 21.37 1.24e+00 6.50e-01 2.97e+02 ... (remaining 39901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.84: 18444 26.84 - 53.67: 405 53.67 - 80.51: 138 80.51 - 107.34: 131 107.34 - 134.18: 31 Dihedral angle restraints: 19149 sinusoidal: 9033 harmonic: 10116 Sorted by residual: dihedral pdb=" N CYS A 383 " pdb=" C CYS A 383 " pdb=" CA CYS A 383 " pdb=" CB CYS A 383 " ideal model delta harmonic sigma weight residual 122.80 96.18 26.62 0 2.50e+00 1.60e-01 1.13e+02 dihedral pdb=" N CYS C 383 " pdb=" C CYS C 383 " pdb=" CA CYS C 383 " pdb=" CB CYS C 383 " ideal model delta harmonic sigma weight residual 122.80 96.19 26.61 0 2.50e+00 1.60e-01 1.13e+02 dihedral pdb=" N CYS B 383 " pdb=" C CYS B 383 " pdb=" CA CYS B 383 " pdb=" CB CYS B 383 " ideal model delta harmonic sigma weight residual 122.80 96.19 26.61 0 2.50e+00 1.60e-01 1.13e+02 ... (remaining 19146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.390: 4771 0.390 - 0.781: 68 0.781 - 1.171: 6 1.171 - 1.561: 0 1.561 - 1.952: 3 Chirality restraints: 4848 Sorted by residual: chirality pdb=" C1 MAN U 5 " pdb=" O6 BMA U 3 " pdb=" C2 MAN U 5 " pdb=" O5 MAN U 5 " both_signs ideal model delta sigma weight residual False 2.40 2.85 -0.45 2.00e-02 2.50e+03 4.96e+02 chirality pdb=" C1 MAN e 4 " pdb=" O3 BMA e 3 " pdb=" C2 MAN e 4 " pdb=" O5 MAN e 4 " both_signs ideal model delta sigma weight residual False 2.40 2.84 -0.44 2.00e-02 2.50e+03 4.80e+02 chirality pdb=" C1 MAN K 5 " pdb=" O6 BMA K 3 " pdb=" C2 MAN K 5 " pdb=" O5 MAN K 5 " both_signs ideal model delta sigma weight residual False 2.40 2.83 -0.43 2.00e-02 2.50e+03 4.72e+02 ... (remaining 4845 not shown) Planarity restraints: 5022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 777 " -0.078 2.00e-02 2.50e+03 4.34e-02 3.76e+01 pdb=" CG TYR A 777 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 777 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR A 777 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A 777 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR A 777 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR A 777 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 777 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 777 " -0.078 2.00e-02 2.50e+03 4.32e-02 3.73e+01 pdb=" CG TYR B 777 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR B 777 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR B 777 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR B 777 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR B 777 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR B 777 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 777 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 777 " 0.078 2.00e-02 2.50e+03 4.31e-02 3.72e+01 pdb=" CG TYR C 777 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR C 777 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR C 777 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR C 777 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR C 777 " -0.028 2.00e-02 2.50e+03 pdb=" CZ TYR C 777 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR C 777 " 0.070 2.00e-02 2.50e+03 ... (remaining 5019 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 7506 2.78 - 3.31: 26115 3.31 - 3.84: 51776 3.84 - 4.37: 63392 4.37 - 4.90: 101827 Nonbonded interactions: 250616 Sorted by model distance: nonbonded pdb=" O5 BMA K 3 " pdb=" O6 BMA K 3 " model vdw 2.256 2.432 nonbonded pdb=" O5 BMA U 3 " pdb=" O6 BMA U 3 " model vdw 2.256 2.432 nonbonded pdb=" O5 BMA e 3 " pdb=" O6 BMA e 3 " model vdw 2.256 2.432 nonbonded pdb=" N ASP B 343 " pdb=" OD1 ASP B 343 " model vdw 2.345 3.120 nonbonded pdb=" N ASP A 343 " pdb=" OD1 ASP A 343 " model vdw 2.346 3.120 ... (remaining 250611 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: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'N' selection = chain 'R' selection = chain 'X' selection = chain 'b' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'O' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'Y' selection = chain 'c' selection = chain 'd' selection = chain 'g' } ncs_group { reference = chain 'F' selection = chain 'P' selection = chain 'Z' } ncs_group { reference = chain 'G' selection = chain 'Q' selection = chain 'a' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'U' selection = chain 'V' selection = chain 'e' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.110 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 71.880 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 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 : 0.026 0.368 29496 Z= 1.384 Angle : 2.053 25.937 40395 Z= 1.283 Chirality : 0.148 1.952 4848 Planarity : 0.009 0.048 4971 Dihedral : 15.995 134.180 12540 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.57 % Favored : 98.35 % Rotamer: Outliers : 0.91 % Allowed : 1.31 % Favored : 97.78 % Cbeta Deviations : 0.62 % 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: 0.58 (0.13), residues: 3447 helix: -0.49 (0.17), residues: 678 sheet: 0.67 (0.17), residues: 846 loop : 0.78 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.005 TRP A1184 HIS 0.009 0.003 HIS C 264 PHE 0.050 0.006 PHE B 473 TYR 0.079 0.011 TYR A 184 ARG 0.012 0.002 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.03216 ( 51) link_NAG-ASN : angle 2.66657 ( 153) link_ALPHA1-6 : bond 0.05256 ( 9) link_ALPHA1-6 : angle 10.66529 ( 27) link_BETA1-4 : bond 0.06237 ( 48) link_BETA1-4 : angle 2.96214 ( 144) link_ALPHA1-2 : bond 0.06670 ( 6) link_ALPHA1-2 : angle 3.34714 ( 18) link_ALPHA1-3 : bond 0.06000 ( 15) link_ALPHA1-3 : angle 3.69857 ( 45) hydrogen bonds : bond 0.15185 ( 1157) hydrogen bonds : angle 7.71982 ( 3024) SS BOND : bond 0.04853 ( 51) SS BOND : angle 3.43679 ( 102) covalent geometry : bond 0.02530 (29316) covalent geometry : angle 2.02009 (39906) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 590 time to evaluate : 2.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 ILE cc_start: 0.8324 (pt) cc_final: 0.8104 (pt) outliers start: 27 outliers final: 4 residues processed: 605 average time/residue: 1.3949 time to fit residues: 993.3491 Evaluate side-chains 326 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 322 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 644 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 291 optimal weight: 0.6980 chunk 261 optimal weight: 0.5980 chunk 145 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 176 optimal weight: 0.7980 chunk 139 optimal weight: 0.5980 chunk 270 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 chunk 313 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 107 GLN A 280 GLN A 521 ASN A 576 GLN A 582 ASN A 681 HIS ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 GLN A1072 ASN A1163 ASN B 107 GLN B 280 GLN B 576 GLN B 582 ASN B 681 HIS B 819 GLN B 832 ASN B 987 GLN B 988 GLN B 994 GLN B1072 ASN C 107 GLN C 280 GLN C 304 GLN C 521 ASN C 576 GLN C 582 ASN C 812 ASN ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 987 GLN C1072 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.156574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122858 restraints weight = 32888.043| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.35 r_work: 0.3381 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 29496 Z= 0.190 Angle : 0.765 16.175 40395 Z= 0.381 Chirality : 0.049 0.247 4848 Planarity : 0.004 0.035 4971 Dihedral : 13.250 116.005 6518 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.32 % Allowed : 10.05 % Favored : 87.63 % Cbeta Deviations : 0.09 % 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: 0.66 (0.14), residues: 3447 helix: 0.68 (0.20), residues: 693 sheet: 0.52 (0.16), residues: 852 loop : 0.45 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 310 HIS 0.007 0.001 HIS C1122 PHE 0.022 0.002 PHE A 850 TYR 0.022 0.002 TYR A 77 ARG 0.007 0.001 ARG B 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00647 ( 51) link_NAG-ASN : angle 3.05042 ( 153) link_ALPHA1-6 : bond 0.00646 ( 9) link_ALPHA1-6 : angle 2.08138 ( 27) link_BETA1-4 : bond 0.01010 ( 48) link_BETA1-4 : angle 2.99108 ( 144) link_ALPHA1-2 : bond 0.00613 ( 6) link_ALPHA1-2 : angle 1.75375 ( 18) link_ALPHA1-3 : bond 0.00983 ( 15) link_ALPHA1-3 : angle 2.27731 ( 45) hydrogen bonds : bond 0.05514 ( 1157) hydrogen bonds : angle 6.17717 ( 3024) SS BOND : bond 0.00291 ( 51) SS BOND : angle 1.38942 ( 102) covalent geometry : bond 0.00416 (29316) covalent geometry : angle 0.71331 (39906) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 414 time to evaluate : 2.935 Fit side-chains revert: symmetry clash REVERT: A 587 LYS cc_start: 0.7593 (ptpp) cc_final: 0.7290 (mptt) REVERT: A 614 ARG cc_start: 0.7903 (mtt90) cc_final: 0.7530 (mtt90) REVERT: A 666 GLU cc_start: 0.7849 (mp0) cc_final: 0.7522 (mp0) REVERT: A 899 THR cc_start: 0.7896 (m) cc_final: 0.7541 (p) REVERT: A 913 MET cc_start: 0.5806 (OUTLIER) cc_final: 0.5367 (mmt) REVERT: A 988 GLN cc_start: 0.7214 (tm130) cc_final: 0.6996 (tt0) REVERT: A 1068 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7961 (t70) REVERT: A 1137 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7954 (mtm) REVERT: B 141 ARG cc_start: 0.7869 (mtt90) cc_final: 0.7084 (mtp180) REVERT: B 369 LYS cc_start: 0.6242 (mptt) cc_final: 0.5974 (mptt) REVERT: B 379 GLU cc_start: 0.7159 (tt0) cc_final: 0.6668 (mm-30) REVERT: B 536 GLU cc_start: 0.6969 (pp20) cc_final: 0.6637 (pp20) REVERT: B 764 PHE cc_start: 0.8218 (t80) cc_final: 0.7856 (t80) REVERT: B 854 LYS cc_start: 0.6762 (tttm) cc_final: 0.6196 (tptp) REVERT: B 899 THR cc_start: 0.7887 (m) cc_final: 0.7584 (p) REVERT: B 909 TYR cc_start: 0.7770 (t80) cc_final: 0.7450 (t80) REVERT: B 1035 LYS cc_start: 0.7859 (mptt) cc_final: 0.7107 (tttm) REVERT: B 1062 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6562 (mp0) REVERT: B 1105 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7777 (mt-10) REVERT: B 1113 ARG cc_start: 0.8155 (mtp180) cc_final: 0.7814 (mtp180) REVERT: B 1148 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: C 141 ARG cc_start: 0.8036 (mmt90) cc_final: 0.7073 (mtp85) REVERT: C 352 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8065 (mt-10) REVERT: C 406 ASN cc_start: 0.7924 (m-40) cc_final: 0.7661 (m-40) REVERT: C 536 GLU cc_start: 0.6720 (pp20) cc_final: 0.6464 (pp20) REVERT: C 587 LYS cc_start: 0.7381 (ptpp) cc_final: 0.7124 (mptt) REVERT: C 614 ARG cc_start: 0.7864 (mtt90) cc_final: 0.7574 (mtt180) REVERT: C 666 GLU cc_start: 0.7688 (mp0) cc_final: 0.7427 (mp0) REVERT: C 725 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7491 (mt-10) REVERT: C 777 TYR cc_start: 0.7934 (m-80) cc_final: 0.7612 (m-80) REVERT: C 823 GLU cc_start: 0.7679 (mm-30) cc_final: 0.6863 (pt0) REVERT: C 826 GLN cc_start: 0.6678 (mm110) cc_final: 0.6414 (mm-40) REVERT: C 849 LEU cc_start: 0.8208 (tp) cc_final: 0.7925 (tt) REVERT: C 854 LYS cc_start: 0.7000 (tttm) cc_final: 0.6290 (tptm) REVERT: C 862 ILE cc_start: 0.6965 (pt) cc_final: 0.6605 (mp) REVERT: C 875 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7135 (mt-10) REVERT: C 899 THR cc_start: 0.8062 (m) cc_final: 0.7655 (p) REVERT: C 1056 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: C 1137 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7984 (mtm) outliers start: 69 outliers final: 16 residues processed: 449 average time/residue: 1.3365 time to fit residues: 710.9862 Evaluate side-chains 339 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 315 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1137 MET Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1137 MET Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 63 optimal weight: 0.9990 chunk 320 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 341 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 79 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 466 GLN A 647 ASN A 681 HIS A 832 ASN B 167 HIS B 194 HIS B 647 ASN B 681 HIS B 819 GLN B 832 ASN B 987 GLN C 167 HIS C 261 GLN C 466 GLN C 987 GLN C1145 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.153888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.120000 restraints weight = 32891.308| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.34 r_work: 0.3341 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 29496 Z= 0.196 Angle : 0.713 15.609 40395 Z= 0.352 Chirality : 0.048 0.238 4848 Planarity : 0.004 0.040 4971 Dihedral : 10.870 94.459 6510 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.09 % Allowed : 11.39 % Favored : 85.52 % Cbeta Deviations : 0.09 % 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: 0.43 (0.14), residues: 3447 helix: 0.76 (0.20), residues: 717 sheet: 0.24 (0.17), residues: 828 loop : 0.26 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 310 HIS 0.006 0.001 HIS C 486 PHE 0.021 0.002 PHE C 473 TYR 0.019 0.002 TYR A 77 ARG 0.005 0.001 ARG A 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00867 ( 51) link_NAG-ASN : angle 2.86361 ( 153) link_ALPHA1-6 : bond 0.00709 ( 9) link_ALPHA1-6 : angle 1.61670 ( 27) link_BETA1-4 : bond 0.00998 ( 48) link_BETA1-4 : angle 2.55507 ( 144) link_ALPHA1-2 : bond 0.00660 ( 6) link_ALPHA1-2 : angle 1.52836 ( 18) link_ALPHA1-3 : bond 0.01112 ( 15) link_ALPHA1-3 : angle 1.66078 ( 45) hydrogen bonds : bond 0.05047 ( 1157) hydrogen bonds : angle 5.92834 ( 3024) SS BOND : bond 0.00437 ( 51) SS BOND : angle 1.76940 ( 102) covalent geometry : bond 0.00444 (29316) covalent geometry : angle 0.66773 (39906) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 366 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8265 (mmmm) REVERT: A 252 GLU cc_start: 0.7952 (pt0) cc_final: 0.7653 (pt0) REVERT: A 303 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7656 (pp) REVERT: A 542 ARG cc_start: 0.8099 (mtt90) cc_final: 0.7824 (mtt90) REVERT: A 548 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7125 (mt) REVERT: A 600 LEU cc_start: 0.8664 (mt) cc_final: 0.8324 (mm) REVERT: A 614 ARG cc_start: 0.7997 (mtt90) cc_final: 0.7569 (mtt90) REVERT: A 666 GLU cc_start: 0.7860 (mp0) cc_final: 0.7542 (mp0) REVERT: A 764 PHE cc_start: 0.8189 (t80) cc_final: 0.7971 (t80) REVERT: A 856 SER cc_start: 0.8726 (t) cc_final: 0.8481 (p) REVERT: A 899 THR cc_start: 0.7951 (m) cc_final: 0.7635 (p) REVERT: A 906 MET cc_start: 0.8316 (ttp) cc_final: 0.7980 (ttm) REVERT: A 913 MET cc_start: 0.5660 (mtt) cc_final: 0.5285 (mmt) REVERT: A 1068 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7933 (t70) REVERT: A 1137 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.7967 (mtm) REVERT: A 1148 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: B 141 ARG cc_start: 0.7905 (mtt90) cc_final: 0.7151 (mtp180) REVERT: B 352 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8192 (mm-30) REVERT: B 369 LYS cc_start: 0.6135 (mptt) cc_final: 0.5900 (mptt) REVERT: B 379 GLU cc_start: 0.7153 (tt0) cc_final: 0.6801 (mm-30) REVERT: B 381 VAL cc_start: 0.7979 (m) cc_final: 0.7620 (p) REVERT: B 536 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6726 (pp20) REVERT: B 542 ARG cc_start: 0.8113 (mtt90) cc_final: 0.7876 (mtt90) REVERT: B 764 PHE cc_start: 0.8378 (t80) cc_final: 0.8096 (t80) REVERT: B 777 TYR cc_start: 0.8005 (m-80) cc_final: 0.7510 (m-10) REVERT: B 796 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8659 (tt0) REVERT: B 812 ASN cc_start: 0.8590 (t0) cc_final: 0.8062 (t0) REVERT: B 854 LYS cc_start: 0.6861 (tttm) cc_final: 0.6169 (tptp) REVERT: B 899 THR cc_start: 0.7942 (m) cc_final: 0.7619 (p) REVERT: B 909 TYR cc_start: 0.7926 (t80) cc_final: 0.7604 (t80) REVERT: B 1035 LYS cc_start: 0.7853 (mptt) cc_final: 0.7194 (tttm) REVERT: B 1062 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6732 (mp0) REVERT: B 1105 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: B 1148 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: C 31 ILE cc_start: 0.8059 (mt) cc_final: 0.7832 (mp) REVERT: C 141 ARG cc_start: 0.8044 (mmt90) cc_final: 0.7074 (mtp180) REVERT: C 252 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.6920 (pt0) REVERT: C 400 LYS cc_start: 0.8309 (mttm) cc_final: 0.8093 (mttp) REVERT: C 406 ASN cc_start: 0.7821 (m-40) cc_final: 0.7509 (m-40) REVERT: C 536 GLU cc_start: 0.6850 (pp20) cc_final: 0.6488 (pp20) REVERT: C 614 ARG cc_start: 0.7868 (mtt90) cc_final: 0.7513 (mtt180) REVERT: C 777 TYR cc_start: 0.8056 (m-80) cc_final: 0.7657 (m-80) REVERT: C 812 ASN cc_start: 0.8491 (t0) cc_final: 0.8258 (t160) REVERT: C 815 GLN cc_start: 0.7283 (mp10) cc_final: 0.6878 (tp-100) REVERT: C 818 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7448 (mt-10) REVERT: C 826 GLN cc_start: 0.7018 (mm110) cc_final: 0.6759 (mm-40) REVERT: C 854 LYS cc_start: 0.7120 (tttm) cc_final: 0.6365 (tptp) REVERT: C 899 THR cc_start: 0.8199 (m) cc_final: 0.7803 (p) REVERT: C 1031 GLN cc_start: 0.7756 (mm110) cc_final: 0.7554 (mm110) REVERT: C 1035 LYS cc_start: 0.7785 (mmtt) cc_final: 0.7314 (tttm) REVERT: C 1056 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7690 (tt0) REVERT: C 1084 GLN cc_start: 0.7702 (tp-100) cc_final: 0.7467 (tp-100) REVERT: C 1137 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8071 (mtm) outliers start: 92 outliers final: 39 residues processed: 424 average time/residue: 1.1855 time to fit residues: 606.7078 Evaluate side-chains 373 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 319 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1084 GLN Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 796 GLN Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1137 MET Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1137 MET Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 257 optimal weight: 0.8980 chunk 162 optimal weight: 0.6980 chunk 340 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 112 optimal weight: 0.2980 chunk 293 optimal weight: 1.9990 chunk 323 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 239 optimal weight: 0.5980 chunk 274 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 HIS A 812 ASN A 832 ASN B 681 HIS ** B 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 832 ASN C 194 HIS C 987 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.154310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.120707 restraints weight = 33078.812| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.33 r_work: 0.3349 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 29496 Z= 0.157 Angle : 0.684 23.080 40395 Z= 0.333 Chirality : 0.047 0.314 4848 Planarity : 0.004 0.043 4971 Dihedral : 8.992 78.928 6510 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.19 % Allowed : 12.30 % Favored : 84.51 % Cbeta Deviations : 0.09 % 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: 0.49 (0.14), residues: 3447 helix: 1.04 (0.20), residues: 702 sheet: 0.28 (0.17), residues: 867 loop : 0.19 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 310 HIS 0.005 0.001 HIS C 486 PHE 0.020 0.002 PHE C 473 TYR 0.013 0.001 TYR B 184 ARG 0.006 0.000 ARG C 887 Details of bonding type rmsd link_NAG-ASN : bond 0.00628 ( 51) link_NAG-ASN : angle 2.81978 ( 153) link_ALPHA1-6 : bond 0.00909 ( 9) link_ALPHA1-6 : angle 1.59504 ( 27) link_BETA1-4 : bond 0.00885 ( 48) link_BETA1-4 : angle 2.32307 ( 144) link_ALPHA1-2 : bond 0.00546 ( 6) link_ALPHA1-2 : angle 1.55747 ( 18) link_ALPHA1-3 : bond 0.01135 ( 15) link_ALPHA1-3 : angle 1.86717 ( 45) hydrogen bonds : bond 0.04561 ( 1157) hydrogen bonds : angle 5.74709 ( 3024) SS BOND : bond 0.00894 ( 51) SS BOND : angle 2.45288 ( 102) covalent geometry : bond 0.00350 (29316) covalent geometry : angle 0.63347 (39906) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 344 time to evaluate : 3.549 Fit side-chains revert: symmetry clash REVERT: A 252 GLU cc_start: 0.7956 (pt0) cc_final: 0.7626 (pt0) REVERT: A 303 ILE cc_start: 0.8069 (pt) cc_final: 0.7707 (pp) REVERT: A 542 ARG cc_start: 0.8084 (mtt90) cc_final: 0.7814 (mtt90) REVERT: A 548 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7157 (mt) REVERT: A 595 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7646 (mmtp) REVERT: A 600 LEU cc_start: 0.8658 (mt) cc_final: 0.8327 (mm) REVERT: A 614 ARG cc_start: 0.7915 (mtt90) cc_final: 0.7491 (mtt90) REVERT: A 666 GLU cc_start: 0.7870 (mp0) cc_final: 0.7535 (mp0) REVERT: A 856 SER cc_start: 0.8716 (t) cc_final: 0.8473 (p) REVERT: A 899 THR cc_start: 0.7999 (m) cc_final: 0.7695 (p) REVERT: A 906 MET cc_start: 0.8316 (ttp) cc_final: 0.8022 (ttm) REVERT: A 913 MET cc_start: 0.5629 (mtt) cc_final: 0.5263 (mmt) REVERT: A 1035 LYS cc_start: 0.7886 (mptt) cc_final: 0.7094 (ttpt) REVERT: A 1068 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7932 (t70) REVERT: A 1137 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8100 (mtp) REVERT: A 1148 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: B 141 ARG cc_start: 0.7930 (mtt90) cc_final: 0.7150 (mtp180) REVERT: B 352 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8183 (mm-30) REVERT: B 379 GLU cc_start: 0.7122 (tt0) cc_final: 0.6749 (mm-30) REVERT: B 381 VAL cc_start: 0.8091 (m) cc_final: 0.7768 (p) REVERT: B 536 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6696 (pp20) REVERT: B 764 PHE cc_start: 0.8438 (t80) cc_final: 0.8147 (t80) REVERT: B 777 TYR cc_start: 0.8031 (m-80) cc_final: 0.7444 (m-10) REVERT: B 899 THR cc_start: 0.7946 (m) cc_final: 0.7651 (p) REVERT: B 909 TYR cc_start: 0.8030 (t80) cc_final: 0.7643 (t80) REVERT: B 1035 LYS cc_start: 0.7857 (mptt) cc_final: 0.7205 (tttm) REVERT: B 1062 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: B 1105 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: B 1137 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8147 (mtp) REVERT: B 1145 ASN cc_start: 0.8570 (m110) cc_final: 0.8244 (m110) REVERT: B 1148 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7574 (mp0) REVERT: C 31 ILE cc_start: 0.8084 (mt) cc_final: 0.7814 (mp) REVERT: C 141 ARG cc_start: 0.8041 (mmt90) cc_final: 0.7162 (mtp85) REVERT: C 400 LYS cc_start: 0.8255 (mttm) cc_final: 0.8047 (mttp) REVERT: C 406 ASN cc_start: 0.7763 (m-40) cc_final: 0.7467 (m-40) REVERT: C 536 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6540 (pp20) REVERT: C 614 ARG cc_start: 0.7862 (mtt90) cc_final: 0.7498 (mtt180) REVERT: C 777 TYR cc_start: 0.8067 (m-80) cc_final: 0.7662 (m-80) REVERT: C 812 ASN cc_start: 0.8494 (t0) cc_final: 0.8258 (t160) REVERT: C 815 GLN cc_start: 0.7278 (mp10) cc_final: 0.6832 (tp-100) REVERT: C 818 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7442 (mt-10) REVERT: C 842 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7257 (mp10) REVERT: C 854 LYS cc_start: 0.7178 (tttm) cc_final: 0.6425 (tptp) REVERT: C 899 THR cc_start: 0.8205 (m) cc_final: 0.7822 (p) REVERT: C 1031 GLN cc_start: 0.7731 (mm110) cc_final: 0.7524 (mm110) REVERT: C 1035 LYS cc_start: 0.7681 (mmtt) cc_final: 0.7273 (tttm) REVERT: C 1056 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: C 1084 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7476 (tp-100) REVERT: C 1137 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8123 (mtm) outliers start: 95 outliers final: 41 residues processed: 401 average time/residue: 1.2957 time to fit residues: 627.3737 Evaluate side-chains 376 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 319 time to evaluate : 3.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1084 GLN Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1137 MET Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1084 GLN Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1137 MET Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 174 optimal weight: 0.0770 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 240 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 167 optimal weight: 0.0980 chunk 298 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN A 812 ASN A 832 ASN B 812 ASN ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 832 ASN C 261 GLN C 987 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.154286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.120708 restraints weight = 32865.388| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.33 r_work: 0.3351 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29496 Z= 0.150 Angle : 0.682 22.398 40395 Z= 0.331 Chirality : 0.046 0.366 4848 Planarity : 0.004 0.044 4971 Dihedral : 7.923 65.088 6510 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.33 % Allowed : 12.74 % Favored : 83.94 % Cbeta Deviations : 0.09 % 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: 0.44 (0.14), residues: 3447 helix: 1.17 (0.20), residues: 702 sheet: 0.13 (0.17), residues: 882 loop : 0.15 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 310 HIS 0.004 0.001 HIS C 208 PHE 0.024 0.001 PHE B 571 TYR 0.016 0.001 TYR C 909 ARG 0.004 0.000 ARG A 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00673 ( 51) link_NAG-ASN : angle 2.82286 ( 153) link_ALPHA1-6 : bond 0.00875 ( 9) link_ALPHA1-6 : angle 1.55731 ( 27) link_BETA1-4 : bond 0.00889 ( 48) link_BETA1-4 : angle 2.26713 ( 144) link_ALPHA1-2 : bond 0.00578 ( 6) link_ALPHA1-2 : angle 1.50521 ( 18) link_ALPHA1-3 : bond 0.01112 ( 15) link_ALPHA1-3 : angle 1.75186 ( 45) hydrogen bonds : bond 0.04409 ( 1157) hydrogen bonds : angle 5.61800 ( 3024) SS BOND : bond 0.00802 ( 51) SS BOND : angle 2.71958 ( 102) covalent geometry : bond 0.00332 (29316) covalent geometry : angle 0.62998 (39906) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 347 time to evaluate : 4.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 542 ARG cc_start: 0.8120 (mtt90) cc_final: 0.7867 (mtt90) REVERT: A 548 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7122 (mt) REVERT: A 600 LEU cc_start: 0.8686 (mt) cc_final: 0.8369 (mm) REVERT: A 614 ARG cc_start: 0.7931 (mtt90) cc_final: 0.7518 (mtt90) REVERT: A 666 GLU cc_start: 0.7909 (mp0) cc_final: 0.7517 (mp0) REVERT: A 764 PHE cc_start: 0.8205 (t80) cc_final: 0.7980 (t80) REVERT: A 856 SER cc_start: 0.8728 (t) cc_final: 0.8467 (p) REVERT: A 899 THR cc_start: 0.7999 (m) cc_final: 0.7740 (p) REVERT: A 906 MET cc_start: 0.8326 (ttp) cc_final: 0.8033 (ttm) REVERT: A 913 MET cc_start: 0.5574 (mtt) cc_final: 0.5122 (mmt) REVERT: A 1035 LYS cc_start: 0.7902 (mptt) cc_final: 0.7133 (ttpt) REVERT: A 1068 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7835 (t70) REVERT: A 1148 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: A 1151 SER cc_start: 0.8719 (m) cc_final: 0.8388 (t) REVERT: B 141 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7102 (mtp85) REVERT: B 352 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8205 (mm-30) REVERT: B 369 LYS cc_start: 0.6395 (mptt) cc_final: 0.6069 (mptp) REVERT: B 379 GLU cc_start: 0.7114 (tt0) cc_final: 0.6728 (mm-30) REVERT: B 381 VAL cc_start: 0.8085 (OUTLIER) cc_final: 0.7799 (p) REVERT: B 536 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6750 (pp20) REVERT: B 764 PHE cc_start: 0.8456 (t80) cc_final: 0.8161 (t80) REVERT: B 777 TYR cc_start: 0.8066 (m-80) cc_final: 0.7463 (m-10) REVERT: B 899 THR cc_start: 0.7989 (m) cc_final: 0.7720 (p) REVERT: B 909 TYR cc_start: 0.7981 (t80) cc_final: 0.7781 (t80) REVERT: B 1035 LYS cc_start: 0.7791 (mptt) cc_final: 0.7228 (tttm) REVERT: B 1062 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6690 (mp0) REVERT: B 1105 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7834 (mt-10) REVERT: B 1145 ASN cc_start: 0.8530 (m110) cc_final: 0.8197 (m110) REVERT: B 1148 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7751 (mt-10) REVERT: C 31 ILE cc_start: 0.8092 (mt) cc_final: 0.7816 (mp) REVERT: C 141 ARG cc_start: 0.8029 (mmt90) cc_final: 0.7166 (mtp85) REVERT: C 252 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.6941 (pt0) REVERT: C 406 ASN cc_start: 0.7773 (m-40) cc_final: 0.7471 (m-40) REVERT: C 536 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6598 (pp20) REVERT: C 614 ARG cc_start: 0.7846 (mtt90) cc_final: 0.7389 (mtt180) REVERT: C 777 TYR cc_start: 0.8099 (m-80) cc_final: 0.7686 (m-80) REVERT: C 815 GLN cc_start: 0.7299 (mp10) cc_final: 0.6821 (tp-100) REVERT: C 818 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7380 (mt-10) REVERT: C 842 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7290 (mp10) REVERT: C 844 ASP cc_start: 0.7096 (m-30) cc_final: 0.6711 (m-30) REVERT: C 854 LYS cc_start: 0.7120 (tttm) cc_final: 0.6370 (tptp) REVERT: C 899 THR cc_start: 0.8236 (m) cc_final: 0.7912 (p) REVERT: C 995 LYS cc_start: 0.7552 (mmtt) cc_final: 0.7295 (mmmt) REVERT: C 1031 GLN cc_start: 0.7626 (mm110) cc_final: 0.7414 (mm110) REVERT: C 1035 LYS cc_start: 0.7800 (mmtt) cc_final: 0.7289 (tttm) REVERT: C 1056 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7672 (tt0) REVERT: C 1068 ASP cc_start: 0.8108 (t70) cc_final: 0.7515 (m-30) REVERT: C 1084 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7465 (tp-100) REVERT: C 1137 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7984 (mtp) outliers start: 99 outliers final: 43 residues processed: 409 average time/residue: 1.1885 time to fit residues: 587.5511 Evaluate side-chains 387 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 329 time to evaluate : 3.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1084 GLN Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1084 GLN Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1084 GLN Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1137 MET Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 165 optimal weight: 1.9990 chunk 300 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 229 optimal weight: 2.9990 chunk 308 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 45 optimal weight: 0.0570 chunk 309 optimal weight: 2.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN A 681 HIS A 812 ASN A 832 ASN B 167 HIS B 427 GLN B 812 ASN ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 832 ASN B1009 GLN C 167 HIS C 261 GLN C 566 GLN C 812 ASN C 987 GLN C1169 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.152069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.118369 restraints weight = 32887.316| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.32 r_work: 0.3319 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 29496 Z= 0.208 Angle : 0.726 27.684 40395 Z= 0.354 Chirality : 0.048 0.373 4848 Planarity : 0.004 0.045 4971 Dihedral : 7.827 64.182 6510 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.73 % Allowed : 13.14 % Favored : 83.13 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.14), residues: 3447 helix: 1.03 (0.20), residues: 702 sheet: 0.10 (0.17), residues: 861 loop : 0.07 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 960 HIS 0.005 0.001 HIS C 486 PHE 0.022 0.002 PHE C 473 TYR 0.018 0.002 TYR B 184 ARG 0.005 0.001 ARG B 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00621 ( 51) link_NAG-ASN : angle 2.75829 ( 153) link_ALPHA1-6 : bond 0.00799 ( 9) link_ALPHA1-6 : angle 1.60298 ( 27) link_BETA1-4 : bond 0.00817 ( 48) link_BETA1-4 : angle 2.32759 ( 144) link_ALPHA1-2 : bond 0.00587 ( 6) link_ALPHA1-2 : angle 1.49863 ( 18) link_ALPHA1-3 : bond 0.01048 ( 15) link_ALPHA1-3 : angle 1.78836 ( 45) hydrogen bonds : bond 0.04819 ( 1157) hydrogen bonds : angle 5.67002 ( 3024) SS BOND : bond 0.00820 ( 51) SS BOND : angle 2.75479 ( 102) covalent geometry : bond 0.00480 (29316) covalent geometry : angle 0.67768 (39906) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 318 time to evaluate : 3.246 Fit side-chains revert: symmetry clash REVERT: A 52 LYS cc_start: 0.6980 (mtpp) cc_final: 0.6598 (mtmt) REVERT: A 542 ARG cc_start: 0.8155 (mtt90) cc_final: 0.7918 (mtt90) REVERT: A 548 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7154 (mt) REVERT: A 600 LEU cc_start: 0.8622 (mt) cc_final: 0.8296 (mm) REVERT: A 614 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7372 (mtt180) REVERT: A 652 ARG cc_start: 0.7376 (mmt90) cc_final: 0.6798 (mmt-90) REVERT: A 666 GLU cc_start: 0.7929 (mp0) cc_final: 0.7562 (mp0) REVERT: A 856 SER cc_start: 0.8730 (t) cc_final: 0.8441 (p) REVERT: A 899 THR cc_start: 0.8048 (m) cc_final: 0.7804 (p) REVERT: A 906 MET cc_start: 0.8345 (ttp) cc_final: 0.8033 (ttm) REVERT: A 913 MET cc_start: 0.5658 (mtt) cc_final: 0.5128 (mmt) REVERT: A 1035 LYS cc_start: 0.7903 (mptt) cc_final: 0.7157 (ttpt) REVERT: A 1068 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7951 (t70) REVERT: A 1148 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: B 141 ARG cc_start: 0.7830 (mtt90) cc_final: 0.7044 (mtp180) REVERT: B 352 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8243 (mm-30) REVERT: B 379 GLU cc_start: 0.7239 (tt0) cc_final: 0.6778 (mm-30) REVERT: B 381 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7870 (p) REVERT: B 509 ASP cc_start: 0.6472 (OUTLIER) cc_final: 0.6053 (p0) REVERT: B 536 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6725 (pp20) REVERT: B 600 LEU cc_start: 0.8510 (mt) cc_final: 0.8076 (mm) REVERT: B 777 TYR cc_start: 0.8180 (m-80) cc_final: 0.7539 (m-10) REVERT: B 812 ASN cc_start: 0.8825 (t0) cc_final: 0.8106 (t160) REVERT: B 899 THR cc_start: 0.7991 (m) cc_final: 0.7706 (p) REVERT: B 909 TYR cc_start: 0.8056 (t80) cc_final: 0.7796 (t80) REVERT: B 1062 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6770 (mp0) REVERT: B 1105 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: B 1145 ASN cc_start: 0.8523 (m110) cc_final: 0.8157 (m110) REVERT: B 1148 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: C 31 ILE cc_start: 0.8119 (mt) cc_final: 0.7824 (mp) REVERT: C 98 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.6917 (pt0) REVERT: C 141 ARG cc_start: 0.8040 (mmt90) cc_final: 0.7140 (mtp180) REVERT: C 161 MET cc_start: 0.7914 (mmp) cc_final: 0.7542 (mmm) REVERT: C 252 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.6967 (pt0) REVERT: C 406 ASN cc_start: 0.7845 (m-40) cc_final: 0.7515 (m-40) REVERT: C 536 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6599 (pp20) REVERT: C 612 SER cc_start: 0.8674 (OUTLIER) cc_final: 0.8356 (m) REVERT: C 614 ARG cc_start: 0.7873 (mtt90) cc_final: 0.7539 (mtt180) REVERT: C 777 TYR cc_start: 0.8189 (m-80) cc_final: 0.7755 (m-80) REVERT: C 812 ASN cc_start: 0.8787 (t0) cc_final: 0.8179 (t160) REVERT: C 815 GLN cc_start: 0.7254 (mp10) cc_final: 0.6749 (tp-100) REVERT: C 818 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7405 (mt-10) REVERT: C 842 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7358 (mp10) REVERT: C 844 ASP cc_start: 0.7221 (m-30) cc_final: 0.6813 (m-30) REVERT: C 899 THR cc_start: 0.8299 (m) cc_final: 0.7998 (p) REVERT: C 995 LYS cc_start: 0.7648 (mmtt) cc_final: 0.7385 (mmmt) REVERT: C 1031 GLN cc_start: 0.7730 (mm110) cc_final: 0.7496 (mm110) REVERT: C 1035 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7342 (tttm) REVERT: C 1056 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: C 1068 ASP cc_start: 0.8110 (t70) cc_final: 0.7494 (m-30) REVERT: C 1084 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7504 (tp-100) outliers start: 111 outliers final: 57 residues processed: 389 average time/residue: 1.3072 time to fit residues: 633.0745 Evaluate side-chains 395 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 320 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 614 ARG Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1084 GLN Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1084 GLN Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1084 GLN Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1162 THR Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 258 optimal weight: 0.9980 chunk 231 optimal weight: 0.5980 chunk 329 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 49 optimal weight: 0.0170 chunk 305 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 252 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 158 optimal weight: 0.5980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN B 167 HIS B 576 GLN ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 HIS C 261 GLN C 987 GLN C1009 GLN C1169 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.154269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.120231 restraints weight = 33023.822| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.36 r_work: 0.3350 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 29496 Z= 0.140 Angle : 0.695 26.901 40395 Z= 0.336 Chirality : 0.046 0.380 4848 Planarity : 0.004 0.050 4971 Dihedral : 7.306 61.375 6510 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.65 % Allowed : 14.65 % Favored : 82.69 % Cbeta Deviations : 0.09 % 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: 0.40 (0.14), residues: 3447 helix: 1.29 (0.20), residues: 684 sheet: 0.06 (0.17), residues: 891 loop : 0.10 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 310 HIS 0.002 0.001 HIS C 167 PHE 0.026 0.001 PHE B 571 TYR 0.011 0.001 TYR B 274 ARG 0.004 0.000 ARG A 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00584 ( 51) link_NAG-ASN : angle 3.34156 ( 153) link_ALPHA1-6 : bond 0.00870 ( 9) link_ALPHA1-6 : angle 1.50578 ( 27) link_BETA1-4 : bond 0.00851 ( 48) link_BETA1-4 : angle 2.16555 ( 144) link_ALPHA1-2 : bond 0.00554 ( 6) link_ALPHA1-2 : angle 1.49006 ( 18) link_ALPHA1-3 : bond 0.01037 ( 15) link_ALPHA1-3 : angle 1.68419 ( 45) hydrogen bonds : bond 0.04268 ( 1157) hydrogen bonds : angle 5.61156 ( 3024) SS BOND : bond 0.00853 ( 51) SS BOND : angle 3.41433 ( 102) covalent geometry : bond 0.00305 (29316) covalent geometry : angle 0.62798 (39906) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 341 time to evaluate : 3.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.6943 (mtpp) cc_final: 0.6501 (mtmt) REVERT: A 542 ARG cc_start: 0.8136 (mtt90) cc_final: 0.7897 (mtt90) REVERT: A 548 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7159 (mt) REVERT: A 600 LEU cc_start: 0.8625 (mt) cc_final: 0.8310 (mm) REVERT: A 614 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7619 (mtt90) REVERT: A 652 ARG cc_start: 0.7368 (mmt90) cc_final: 0.6814 (mmt-90) REVERT: A 666 GLU cc_start: 0.7940 (mp0) cc_final: 0.7564 (mp0) REVERT: A 856 SER cc_start: 0.8729 (t) cc_final: 0.8440 (p) REVERT: A 899 THR cc_start: 0.8013 (m) cc_final: 0.7801 (p) REVERT: A 906 MET cc_start: 0.8312 (ttp) cc_final: 0.8035 (ttm) REVERT: A 913 MET cc_start: 0.5625 (mtt) cc_final: 0.5101 (mmt) REVERT: A 1035 LYS cc_start: 0.7835 (mptt) cc_final: 0.7149 (ttpt) REVERT: A 1068 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7856 (t70) REVERT: A 1151 SER cc_start: 0.8716 (m) cc_final: 0.8434 (t) REVERT: B 141 ARG cc_start: 0.7779 (mtt90) cc_final: 0.7044 (mtp180) REVERT: B 252 GLU cc_start: 0.7833 (pt0) cc_final: 0.7301 (pt0) REVERT: B 379 GLU cc_start: 0.7240 (tt0) cc_final: 0.6749 (mm-30) REVERT: B 381 VAL cc_start: 0.8119 (OUTLIER) cc_final: 0.7821 (p) REVERT: B 487 ASN cc_start: 0.6873 (OUTLIER) cc_final: 0.6156 (t0) REVERT: B 536 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6837 (pp20) REVERT: B 600 LEU cc_start: 0.8471 (mt) cc_final: 0.8103 (mm) REVERT: B 764 PHE cc_start: 0.8371 (t80) cc_final: 0.7941 (t80) REVERT: B 777 TYR cc_start: 0.8083 (m-80) cc_final: 0.7466 (m-10) REVERT: B 812 ASN cc_start: 0.8799 (t0) cc_final: 0.8118 (t160) REVERT: B 899 THR cc_start: 0.8093 (m) cc_final: 0.7807 (p) REVERT: B 1062 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6644 (mp0) REVERT: B 1105 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7842 (mt-10) REVERT: B 1145 ASN cc_start: 0.8530 (m110) cc_final: 0.8218 (m110) REVERT: B 1148 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: C 31 ILE cc_start: 0.8077 (mt) cc_final: 0.7775 (mp) REVERT: C 98 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.6786 (pm20) REVERT: C 141 ARG cc_start: 0.8092 (mmt90) cc_final: 0.7192 (mtp85) REVERT: C 161 MET cc_start: 0.8010 (mmp) cc_final: 0.7747 (mmm) REVERT: C 252 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.6933 (pt0) REVERT: C 406 ASN cc_start: 0.7775 (m-40) cc_final: 0.7452 (m-40) REVERT: C 536 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6601 (pp20) REVERT: C 614 ARG cc_start: 0.7867 (mtt90) cc_final: 0.7542 (mtt180) REVERT: C 765 ASN cc_start: 0.8043 (t0) cc_final: 0.7296 (m-40) REVERT: C 777 TYR cc_start: 0.8144 (m-80) cc_final: 0.7717 (m-80) REVERT: C 812 ASN cc_start: 0.8782 (t0) cc_final: 0.8179 (t160) REVERT: C 815 GLN cc_start: 0.7315 (mp10) cc_final: 0.6766 (tp-100) REVERT: C 818 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7369 (mt-10) REVERT: C 842 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7353 (mp10) REVERT: C 844 ASP cc_start: 0.7187 (m-30) cc_final: 0.6774 (m-30) REVERT: C 899 THR cc_start: 0.8299 (m) cc_final: 0.8039 (p) REVERT: C 995 LYS cc_start: 0.7621 (mmtt) cc_final: 0.7367 (mmmt) REVERT: C 1031 GLN cc_start: 0.7583 (mm110) cc_final: 0.7355 (mm110) REVERT: C 1035 LYS cc_start: 0.7881 (mmtt) cc_final: 0.7406 (tttm) REVERT: C 1056 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7725 (tt0) REVERT: C 1068 ASP cc_start: 0.8125 (t70) cc_final: 0.7534 (m-30) REVERT: C 1084 GLN cc_start: 0.7752 (tp-100) cc_final: 0.7502 (tp-100) outliers start: 79 outliers final: 40 residues processed: 390 average time/residue: 1.2022 time to fit residues: 565.9659 Evaluate side-chains 377 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 322 time to evaluate : 3.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 614 ARG Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1084 GLN Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 53 optimal weight: 5.9990 chunk 337 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 252 optimal weight: 0.1980 chunk 159 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 267 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 299 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 566 GLN A 681 HIS A 832 ASN A1009 GLN ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 832 ASN B1009 GLN C 167 HIS C 261 GLN C 427 GLN C 987 GLN C1009 GLN C1169 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.152082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.117960 restraints weight = 33204.669| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.36 r_work: 0.3319 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 29496 Z= 0.196 Angle : 0.727 27.016 40395 Z= 0.354 Chirality : 0.048 0.399 4848 Planarity : 0.004 0.047 4971 Dihedral : 7.388 61.896 6510 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.23 % Allowed : 14.31 % Favored : 82.46 % Cbeta Deviations : 0.09 % 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: 0.24 (0.14), residues: 3447 helix: 1.00 (0.20), residues: 702 sheet: 0.10 (0.16), residues: 906 loop : -0.03 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 960 HIS 0.004 0.001 HIS C 208 PHE 0.026 0.002 PHE B 571 TYR 0.013 0.002 TYR C 909 ARG 0.005 0.001 ARG A 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 51) link_NAG-ASN : angle 3.21857 ( 153) link_ALPHA1-6 : bond 0.00780 ( 9) link_ALPHA1-6 : angle 1.60029 ( 27) link_BETA1-4 : bond 0.00772 ( 48) link_BETA1-4 : angle 2.22112 ( 144) link_ALPHA1-2 : bond 0.00584 ( 6) link_ALPHA1-2 : angle 1.47975 ( 18) link_ALPHA1-3 : bond 0.00971 ( 15) link_ALPHA1-3 : angle 1.70118 ( 45) hydrogen bonds : bond 0.04674 ( 1157) hydrogen bonds : angle 5.68457 ( 3024) SS BOND : bond 0.00896 ( 51) SS BOND : angle 3.30522 ( 102) covalent geometry : bond 0.00456 (29316) covalent geometry : angle 0.66646 (39906) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 313 time to evaluate : 3.075 Fit side-chains revert: symmetry clash REVERT: A 52 LYS cc_start: 0.7047 (mtpp) cc_final: 0.6655 (mtmt) REVERT: A 542 ARG cc_start: 0.8158 (mtt90) cc_final: 0.7938 (mtt90) REVERT: A 548 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7172 (mt) REVERT: A 600 LEU cc_start: 0.8635 (mt) cc_final: 0.8322 (mm) REVERT: A 614 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7486 (mtt180) REVERT: A 652 ARG cc_start: 0.7332 (mmt90) cc_final: 0.6806 (mmt-90) REVERT: A 666 GLU cc_start: 0.7954 (mp0) cc_final: 0.7539 (mp0) REVERT: A 856 SER cc_start: 0.8739 (t) cc_final: 0.8450 (p) REVERT: A 899 THR cc_start: 0.8078 (m) cc_final: 0.7864 (p) REVERT: A 906 MET cc_start: 0.8340 (ttp) cc_final: 0.7996 (ttm) REVERT: A 913 MET cc_start: 0.5645 (mtt) cc_final: 0.5138 (mmt) REVERT: A 1035 LYS cc_start: 0.7886 (mptt) cc_final: 0.7188 (ttpt) REVERT: A 1068 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7780 (t70) REVERT: B 141 ARG cc_start: 0.7825 (mtt90) cc_final: 0.7059 (mtp180) REVERT: B 252 GLU cc_start: 0.7904 (pt0) cc_final: 0.7366 (pt0) REVERT: B 319 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8467 (mp10) REVERT: B 379 GLU cc_start: 0.7305 (tt0) cc_final: 0.6795 (mm-30) REVERT: B 381 VAL cc_start: 0.8086 (OUTLIER) cc_final: 0.7767 (p) REVERT: B 487 ASN cc_start: 0.7121 (OUTLIER) cc_final: 0.6509 (t0) REVERT: B 488 LEU cc_start: 0.6594 (tp) cc_final: 0.6344 (tt) REVERT: B 509 ASP cc_start: 0.6090 (OUTLIER) cc_final: 0.5774 (p0) REVERT: B 536 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6892 (pp20) REVERT: B 600 LEU cc_start: 0.8496 (mt) cc_final: 0.8123 (mm) REVERT: B 777 TYR cc_start: 0.8214 (m-80) cc_final: 0.7546 (m-10) REVERT: B 812 ASN cc_start: 0.8845 (t0) cc_final: 0.8130 (OUTLIER) REVERT: B 899 THR cc_start: 0.8182 (m) cc_final: 0.7872 (p) REVERT: B 1062 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6774 (mp0) REVERT: B 1105 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7884 (mt-10) REVERT: B 1145 ASN cc_start: 0.8522 (m110) cc_final: 0.8169 (m110) REVERT: B 1148 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: C 31 ILE cc_start: 0.8106 (mt) cc_final: 0.7816 (mp) REVERT: C 141 ARG cc_start: 0.8064 (mmt90) cc_final: 0.7186 (mtp85) REVERT: C 161 MET cc_start: 0.7937 (mmp) cc_final: 0.7513 (mmp) REVERT: C 252 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.6963 (pt0) REVERT: C 406 ASN cc_start: 0.7785 (m-40) cc_final: 0.7470 (m-40) REVERT: C 536 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6727 (pp20) REVERT: C 614 ARG cc_start: 0.7905 (mtt90) cc_final: 0.7585 (mtt180) REVERT: C 765 ASN cc_start: 0.8035 (t0) cc_final: 0.7393 (m-40) REVERT: C 777 TYR cc_start: 0.8225 (m-80) cc_final: 0.7824 (m-80) REVERT: C 815 GLN cc_start: 0.7334 (mp10) cc_final: 0.6797 (tp-100) REVERT: C 818 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7394 (mt-10) REVERT: C 842 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7432 (mp10) REVERT: C 844 ASP cc_start: 0.7248 (m-30) cc_final: 0.6844 (m-30) REVERT: C 899 THR cc_start: 0.8277 (m) cc_final: 0.8022 (p) REVERT: C 995 LYS cc_start: 0.7702 (mmtt) cc_final: 0.7393 (mmmt) REVERT: C 1031 GLN cc_start: 0.7679 (mm110) cc_final: 0.7441 (mm110) REVERT: C 1035 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7457 (tttm) REVERT: C 1056 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7746 (tt0) REVERT: C 1068 ASP cc_start: 0.8161 (t70) cc_final: 0.7572 (m-30) REVERT: C 1084 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7505 (tp-100) outliers start: 96 outliers final: 51 residues processed: 375 average time/residue: 1.2201 time to fit residues: 567.6797 Evaluate side-chains 371 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 304 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 614 ARG Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1084 GLN Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 319 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1084 GLN Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1084 GLN Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 90 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 279 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 138 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 167 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 chunk 295 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN ** B 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 987 GLN ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.152748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.118784 restraints weight = 33018.693| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.35 r_work: 0.3329 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 29496 Z= 0.177 Angle : 0.721 27.424 40395 Z= 0.352 Chirality : 0.047 0.414 4848 Planarity : 0.004 0.049 4971 Dihedral : 7.278 60.971 6510 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.82 % Allowed : 14.65 % Favored : 82.53 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 3447 helix: 1.15 (0.20), residues: 684 sheet: 0.06 (0.16), residues: 906 loop : -0.04 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 960 HIS 0.003 0.001 HIS C 208 PHE 0.024 0.002 PHE A 473 TYR 0.010 0.001 TYR B 928 ARG 0.004 0.000 ARG C 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 51) link_NAG-ASN : angle 3.10298 ( 153) link_ALPHA1-6 : bond 0.00791 ( 9) link_ALPHA1-6 : angle 1.54386 ( 27) link_BETA1-4 : bond 0.00759 ( 48) link_BETA1-4 : angle 2.14646 ( 144) link_ALPHA1-2 : bond 0.00570 ( 6) link_ALPHA1-2 : angle 1.48806 ( 18) link_ALPHA1-3 : bond 0.00955 ( 15) link_ALPHA1-3 : angle 1.67827 ( 45) hydrogen bonds : bond 0.04559 ( 1157) hydrogen bonds : angle 5.73520 ( 3024) SS BOND : bond 0.00986 ( 51) SS BOND : angle 3.51940 ( 102) covalent geometry : bond 0.00409 (29316) covalent geometry : angle 0.66007 (39906) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 310 time to evaluate : 3.063 Fit side-chains REVERT: A 52 LYS cc_start: 0.7022 (mtpp) cc_final: 0.6553 (mtmt) REVERT: A 548 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7170 (mt) REVERT: A 600 LEU cc_start: 0.8633 (mt) cc_final: 0.8316 (mm) REVERT: A 614 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7685 (mtt90) REVERT: A 652 ARG cc_start: 0.7262 (mmt90) cc_final: 0.6743 (mmt-90) REVERT: A 832 ASN cc_start: 0.8589 (m-40) cc_final: 0.8346 (m-40) REVERT: A 856 SER cc_start: 0.8737 (t) cc_final: 0.8442 (p) REVERT: A 899 THR cc_start: 0.8097 (m) cc_final: 0.7894 (p) REVERT: A 906 MET cc_start: 0.8313 (ttp) cc_final: 0.7974 (ttm) REVERT: A 913 MET cc_start: 0.5614 (OUTLIER) cc_final: 0.5123 (mmt) REVERT: A 1035 LYS cc_start: 0.7868 (mptt) cc_final: 0.7183 (ttpt) REVERT: A 1068 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7871 (t70) REVERT: A 1151 SER cc_start: 0.8732 (m) cc_final: 0.8416 (t) REVERT: B 141 ARG cc_start: 0.7810 (mtt90) cc_final: 0.7054 (mtp180) REVERT: B 252 GLU cc_start: 0.7898 (pt0) cc_final: 0.7364 (pt0) REVERT: B 319 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8435 (mp10) REVERT: B 379 GLU cc_start: 0.7353 (tt0) cc_final: 0.6775 (mm-30) REVERT: B 381 VAL cc_start: 0.8094 (OUTLIER) cc_final: 0.7771 (p) REVERT: B 487 ASN cc_start: 0.7283 (OUTLIER) cc_final: 0.6613 (t0) REVERT: B 488 LEU cc_start: 0.6567 (tp) cc_final: 0.6327 (tt) REVERT: B 536 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6905 (pp20) REVERT: B 600 LEU cc_start: 0.8480 (mt) cc_final: 0.8100 (mm) REVERT: B 764 PHE cc_start: 0.8386 (t80) cc_final: 0.7967 (t80) REVERT: B 812 ASN cc_start: 0.8834 (t0) cc_final: 0.8192 (t160) REVERT: B 899 THR cc_start: 0.8220 (m) cc_final: 0.7932 (p) REVERT: B 1062 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6765 (mp0) REVERT: B 1105 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7867 (mt-10) REVERT: B 1145 ASN cc_start: 0.8519 (m110) cc_final: 0.8192 (m110) REVERT: B 1148 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7685 (tt0) REVERT: C 31 ILE cc_start: 0.8090 (mt) cc_final: 0.7795 (mp) REVERT: C 141 ARG cc_start: 0.8109 (mmt90) cc_final: 0.7201 (mtp85) REVERT: C 161 MET cc_start: 0.7983 (mmp) cc_final: 0.7574 (mmp) REVERT: C 252 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.6919 (pt0) REVERT: C 406 ASN cc_start: 0.7763 (m-40) cc_final: 0.7454 (m-40) REVERT: C 536 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6741 (pp20) REVERT: C 614 ARG cc_start: 0.7899 (mtt90) cc_final: 0.7582 (mtt180) REVERT: C 765 ASN cc_start: 0.8021 (t0) cc_final: 0.7386 (m-40) REVERT: C 777 TYR cc_start: 0.8204 (m-80) cc_final: 0.7798 (m-80) REVERT: C 815 GLN cc_start: 0.7335 (mp10) cc_final: 0.6793 (tp-100) REVERT: C 818 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: C 842 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7434 (mp10) REVERT: C 844 ASP cc_start: 0.7244 (m-30) cc_final: 0.6835 (m-30) REVERT: C 899 THR cc_start: 0.8279 (m) cc_final: 0.8029 (p) REVERT: C 995 LYS cc_start: 0.7742 (mmtt) cc_final: 0.7418 (mmmt) REVERT: C 1031 GLN cc_start: 0.7661 (mm110) cc_final: 0.7426 (mm110) REVERT: C 1035 LYS cc_start: 0.7932 (mmtt) cc_final: 0.7447 (tttm) REVERT: C 1056 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: C 1068 ASP cc_start: 0.8155 (t70) cc_final: 0.7565 (m-30) REVERT: C 1084 GLN cc_start: 0.7760 (tp-100) cc_final: 0.7503 (tp-100) outliers start: 84 outliers final: 54 residues processed: 361 average time/residue: 1.4044 time to fit residues: 616.1536 Evaluate side-chains 375 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 305 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 614 ARG Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 319 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1084 GLN Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain C residue 1056 GLN Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1162 THR Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 103 optimal weight: 2.9990 chunk 188 optimal weight: 0.5980 chunk 319 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 292 optimal weight: 3.9990 chunk 256 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN B 167 HIS ** B 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 832 ASN B1009 GLN C 261 GLN C 733 GLN ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1169 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.151708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.118198 restraints weight = 32894.671| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.31 r_work: 0.3316 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.146 29496 Z= 0.220 Angle : 0.760 27.647 40395 Z= 0.372 Chirality : 0.049 0.408 4848 Planarity : 0.005 0.047 4971 Dihedral : 7.465 61.664 6510 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.89 % Allowed : 14.78 % Favored : 82.33 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.12 (0.14), residues: 3447 helix: 0.93 (0.20), residues: 702 sheet: 0.03 (0.17), residues: 891 loop : -0.13 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 960 HIS 0.004 0.001 HIS C 208 PHE 0.025 0.002 PHE C 473 TYR 0.021 0.002 TYR B 777 ARG 0.005 0.001 ARG A 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00567 ( 51) link_NAG-ASN : angle 3.18592 ( 153) link_ALPHA1-6 : bond 0.00725 ( 9) link_ALPHA1-6 : angle 1.61196 ( 27) link_BETA1-4 : bond 0.00728 ( 48) link_BETA1-4 : angle 2.18342 ( 144) link_ALPHA1-2 : bond 0.00577 ( 6) link_ALPHA1-2 : angle 1.49591 ( 18) link_ALPHA1-3 : bond 0.00919 ( 15) link_ALPHA1-3 : angle 1.69478 ( 45) hydrogen bonds : bond 0.04847 ( 1157) hydrogen bonds : angle 5.81182 ( 3024) SS BOND : bond 0.01094 ( 51) SS BOND : angle 3.61430 ( 102) covalent geometry : bond 0.00516 (29316) covalent geometry : angle 0.69984 (39906) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 304 time to evaluate : 2.942 Fit side-chains REVERT: A 52 LYS cc_start: 0.7145 (mtpp) cc_final: 0.6658 (mtmt) REVERT: A 548 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7175 (mt) REVERT: A 600 LEU cc_start: 0.8641 (mt) cc_final: 0.8318 (mm) REVERT: A 614 ARG cc_start: 0.8018 (mtt90) cc_final: 0.7579 (mtt180) REVERT: A 652 ARG cc_start: 0.7328 (mmt90) cc_final: 0.6814 (mmt-90) REVERT: A 856 SER cc_start: 0.8738 (t) cc_final: 0.8435 (p) REVERT: A 913 MET cc_start: 0.5767 (OUTLIER) cc_final: 0.5195 (mmt) REVERT: A 1035 LYS cc_start: 0.7899 (mptt) cc_final: 0.7196 (ttpt) REVERT: A 1068 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7953 (t70) REVERT: B 141 ARG cc_start: 0.7815 (mtt90) cc_final: 0.7051 (mtp180) REVERT: B 252 GLU cc_start: 0.7913 (pt0) cc_final: 0.7374 (pt0) REVERT: B 381 VAL cc_start: 0.8182 (OUTLIER) cc_final: 0.7814 (p) REVERT: B 487 ASN cc_start: 0.7275 (OUTLIER) cc_final: 0.6787 (t0) REVERT: B 488 LEU cc_start: 0.6619 (tp) cc_final: 0.6360 (tt) REVERT: B 509 ASP cc_start: 0.6106 (OUTLIER) cc_final: 0.5785 (p0) REVERT: B 536 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6881 (pp20) REVERT: B 600 LEU cc_start: 0.8487 (mt) cc_final: 0.8111 (mm) REVERT: B 764 PHE cc_start: 0.8332 (t80) cc_final: 0.7877 (t80) REVERT: B 899 THR cc_start: 0.8207 (m) cc_final: 0.7941 (p) REVERT: B 1062 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: B 1105 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7903 (mt-10) REVERT: B 1145 ASN cc_start: 0.8521 (m110) cc_final: 0.8158 (m110) REVERT: B 1148 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: C 31 ILE cc_start: 0.8135 (mt) cc_final: 0.7834 (mp) REVERT: C 141 ARG cc_start: 0.8031 (mmt90) cc_final: 0.7149 (mtp85) REVERT: C 161 MET cc_start: 0.7940 (mmp) cc_final: 0.7537 (mmm) REVERT: C 252 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.6944 (pt0) REVERT: C 406 ASN cc_start: 0.7770 (m-40) cc_final: 0.7462 (m-40) REVERT: C 536 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6733 (pp20) REVERT: C 566 GLN cc_start: 0.8211 (mt0) cc_final: 0.7933 (mt0) REVERT: C 614 ARG cc_start: 0.7900 (mtt90) cc_final: 0.7576 (mtt180) REVERT: C 765 ASN cc_start: 0.8022 (t0) cc_final: 0.7397 (m-40) REVERT: C 777 TYR cc_start: 0.8289 (m-80) cc_final: 0.7873 (m-80) REVERT: C 815 GLN cc_start: 0.7416 (mp10) cc_final: 0.6843 (tp-100) REVERT: C 818 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7372 (mt-10) REVERT: C 842 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7464 (mp10) REVERT: C 844 ASP cc_start: 0.7245 (m-30) cc_final: 0.6834 (m-30) REVERT: C 899 THR cc_start: 0.8271 (m) cc_final: 0.8017 (p) REVERT: C 995 LYS cc_start: 0.7785 (mmtt) cc_final: 0.7460 (mmmt) REVERT: C 1031 GLN cc_start: 0.7684 (mm110) cc_final: 0.7444 (mm110) REVERT: C 1035 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7384 (tttm) REVERT: C 1068 ASP cc_start: 0.8138 (t70) cc_final: 0.7555 (m-30) REVERT: C 1084 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7509 (tp-100) outliers start: 86 outliers final: 57 residues processed: 358 average time/residue: 1.6319 time to fit residues: 711.2279 Evaluate side-chains 371 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 298 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1084 GLN Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1084 GLN Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 852 SER Chi-restraints excluded: chain C residue 1035 LYS Chi-restraints excluded: chain C residue 1084 GLN Chi-restraints excluded: chain C residue 1094 LEU Chi-restraints excluded: chain C residue 1162 THR Chi-restraints excluded: chain C residue 1209 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.8611 > 50: distance: 42 - 80: 10.208 distance: 45 - 77: 9.907 distance: 53 - 67: 3.739 distance: 66 - 71: 15.229 distance: 71 - 72: 14.382 distance: 72 - 73: 9.502 distance: 72 - 75: 7.956 distance: 73 - 74: 8.417 distance: 73 - 77: 20.988 distance: 75 - 76: 24.846 distance: 77 - 78: 6.090 distance: 78 - 79: 7.521 distance: 78 - 81: 5.923 distance: 79 - 80: 6.154 distance: 79 - 82: 7.760 distance: 82 - 83: 3.836 distance: 83 - 84: 8.506 distance: 83 - 86: 3.866 distance: 84 - 85: 12.202 distance: 84 - 89: 7.870 distance: 86 - 87: 5.966 distance: 86 - 88: 11.785 distance: 90 - 91: 14.362 distance: 90 - 93: 4.807 distance: 91 - 92: 8.241 distance: 91 - 97: 11.385 distance: 93 - 94: 5.817 distance: 93 - 95: 8.632 distance: 97 - 98: 9.264 distance: 97 - 238: 7.635 distance: 98 - 99: 10.640 distance: 98 - 101: 11.878 distance: 99 - 100: 11.611 distance: 99 - 108: 40.586 distance: 102 - 103: 16.182 distance: 103 - 104: 6.874 distance: 104 - 105: 8.075 distance: 105 - 106: 6.424 distance: 105 - 107: 3.750 distance: 108 - 109: 9.654 distance: 109 - 110: 15.684 distance: 109 - 112: 10.196 distance: 110 - 111: 9.612 distance: 110 - 117: 9.896 distance: 112 - 113: 8.540 distance: 113 - 114: 6.372 distance: 114 - 115: 7.441 distance: 115 - 116: 14.995 distance: 117 - 118: 17.297 distance: 118 - 119: 28.178 distance: 118 - 121: 4.050 distance: 119 - 120: 36.839 distance: 119 - 125: 22.956 distance: 121 - 122: 7.465 distance: 121 - 123: 13.259 distance: 122 - 124: 12.342 distance: 125 - 126: 30.039 distance: 126 - 127: 26.165 distance: 126 - 129: 38.825 distance: 127 - 128: 40.022 distance: 127 - 137: 14.838 distance: 129 - 130: 8.076 distance: 130 - 131: 23.839 distance: 130 - 132: 13.615 distance: 131 - 133: 13.416 distance: 132 - 134: 18.578 distance: 133 - 135: 7.552 distance: 134 - 135: 18.246 distance: 135 - 136: 15.066 distance: 137 - 138: 16.221 distance: 137 - 143: 24.907 distance: 138 - 139: 30.801 distance: 138 - 141: 22.012 distance: 139 - 140: 21.817 distance: 139 - 144: 27.474 distance: 141 - 142: 10.876 distance: 142 - 143: 16.002 distance: 144 - 145: 16.337 distance: 145 - 146: 15.705 distance: 145 - 148: 33.582 distance: 146 - 147: 17.618 distance: 146 - 149: 11.966 distance: 149 - 162: 3.432