Starting phenix.real_space_refine on Sun Sep 13 07:11:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6opo_20151/09_2026/6opo_20151.cif Found real_map, /net/cci-nas-00/data/ceres_data/6opo_20151/09_2026/6opo_20151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6opo_20151/09_2026/6opo_20151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6opo_20151/09_2026/6opo_20151.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6opo_20151/09_2026/6opo_20151.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6opo_20151/09_2026/6opo_20151.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6opo_20151/09_2026/6opo_20151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6opo_20151/09_2026/6opo_20151.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.090 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 114 5.16 5 C 13422 2.51 5 N 3588 2.21 5 O 4317 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21441 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3004 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 22, 'TRANS': 361} Chain breaks: 2 Chain: "L" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 102} Chain: "B" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1089 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 1 Chain: "C" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "D" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3004 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 22, 'TRANS': 361} Chain breaks: 2 Chain: "E" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 102} Chain: "F" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1089 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 1 Chain: "G" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "I" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3004 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 22, 'TRANS': 361} Chain breaks: 2 Chain: "K" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 102} Chain: "M" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1089 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 1 Chain: "N" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "O" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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 chiralities: 5 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 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 chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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 chiralities: 5 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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 chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 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 chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'LMT': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'LMT': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'LMT': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.75, per 1000 atoms: 0.22 Number of scatterers: 21441 At special positions: 0 Unit cell: (155.89, 157.2, 144.1, 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 114 16.00 O 4317 8.00 N 3588 7.00 C 13422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.11 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.18 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 84 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.11 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.04 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.02 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.18 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.05 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 84 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.02 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.11 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.04 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.04 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.02 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS M 605 " distance=2.18 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.05 Simple disulfide: pdb=" SG CYS M 598 " - pdb=" SG CYS M 604 " distance=2.03 Simple disulfide: pdb=" SG CYS N 16 " - pdb=" SG CYS N 84 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.02 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 R 4 " - " MAN R 5 " " MAN b 4 " - " MAN b 5 " " MAN l 4 " - " MAN l 5 " ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA b 3 " - " MAN b 4 " " BMA l 3 " - " MAN l 4 " BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 617 " - " ASN A 339 " " NAG A 624 " - " ASN A 397 " " NAG A 628 " - " ASN A 448 " " NAG B 702 " - " ASN B 611 " " NAG B 703 " - " ASN B 616 " " NAG D 601 " - " ASN D 88 " " NAG D 617 " - " ASN D 339 " " NAG D 624 " - " ASN D 397 " " NAG D 628 " - " ASN D 448 " " NAG F 702 " - " ASN F 611 " " NAG F 703 " - " ASN F 616 " " NAG J 601 " - " ASN J 88 " " NAG J 617 " - " ASN J 339 " " NAG J 624 " - " ASN J 397 " " NAG J 628 " - " ASN J 448 " " NAG M 702 " - " ASN M 611 " " NAG M 703 " - " ASN M 616 " " NAG P 1 " - " ASN A 234 " " NAG Q 1 " - " ASN A 241 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN A 276 " " NAG T 1 " - " ASN A 295 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 362 " " NAG W 1 " - " ASN A 386 " " NAG X 1 " - " ASN A 392 " " NAG Y 1 " - " ASN A 413 " " NAG Z 1 " - " ASN D 234 " " NAG a 1 " - " ASN D 241 " " NAG b 1 " - " ASN D 262 " " NAG c 1 " - " ASN D 276 " " NAG d 1 " - " ASN D 295 " " NAG e 1 " - " ASN D 332 " " NAG f 1 " - " ASN D 362 " " NAG g 1 " - " ASN D 386 " " NAG h 1 " - " ASN D 392 " " NAG i 1 " - " ASN D 413 " " NAG j 1 " - " ASN J 234 " " NAG k 1 " - " ASN J 241 " " NAG l 1 " - " ASN J 262 " " NAG m 1 " - " ASN J 276 " " NAG n 1 " - " ASN J 295 " " NAG o 1 " - " ASN J 332 " " NAG p 1 " - " ASN J 362 " " NAG q 1 " - " ASN J 386 " " NAG r 1 " - " ASN J 392 " " NAG s 1 " - " ASN J 413 " Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 813.2 milliseconds 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4746 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 24.0% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 64 through 72 removed outlier: 3.877A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.843A pdb=" N ASN A 98 " --> pdb=" O MET A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 114 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.667A pdb=" N ASN A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 514 through 518 removed outlier: 3.642A pdb=" N PHE B 518 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 547 Processing helix chain 'B' and resid 565 through 593 removed outlier: 4.216A pdb=" N THR B 569 " --> pdb=" O MET B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'C' and resid 58 through 64 removed outlier: 4.225A pdb=" N ASP C 63 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 99 through 100C Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.877A pdb=" N HIS D 72 " --> pdb=" O VAL D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 98 removed outlier: 3.843A pdb=" N ASN D 98 " --> pdb=" O MET D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 114 Processing helix chain 'D' and resid 335 through 353 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 474 through 484 removed outlier: 3.667A pdb=" N ASN D 478 " --> pdb=" O ASN D 474 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'F' and resid 514 through 518 removed outlier: 3.642A pdb=" N PHE F 518 " --> pdb=" O LEU F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 547 Processing helix chain 'F' and resid 565 through 593 removed outlier: 4.217A pdb=" N THR F 569 " --> pdb=" O MET F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 597 Processing helix chain 'F' and resid 618 through 626 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 661 Processing helix chain 'G' and resid 58 through 64 removed outlier: 4.225A pdb=" N ASP G 63 " --> pdb=" O SER G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 79 Processing helix chain 'I' and resid 28 through 30 No H-bonds generated for 'chain 'I' and resid 28 through 30' Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 99 through 100C Processing helix chain 'J' and resid 64 through 72 removed outlier: 3.877A pdb=" N HIS J 72 " --> pdb=" O VAL J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 98 removed outlier: 3.843A pdb=" N ASN J 98 " --> pdb=" O MET J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 114 Processing helix chain 'J' and resid 335 through 353 Processing helix chain 'J' and resid 368 through 373 Processing helix chain 'J' and resid 387 through 391 Processing helix chain 'J' and resid 474 through 484 removed outlier: 3.667A pdb=" N ASN J 478 " --> pdb=" O ASN J 474 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU J 482 " --> pdb=" O ASN J 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'M' and resid 514 through 518 removed outlier: 3.642A pdb=" N PHE M 518 " --> pdb=" O LEU M 515 " (cutoff:3.500A) Processing helix chain 'M' and resid 529 through 547 Processing helix chain 'M' and resid 565 through 593 removed outlier: 4.217A pdb=" N THR M 569 " --> pdb=" O MET M 565 " (cutoff:3.500A) Processing helix chain 'M' and resid 594 through 597 Processing helix chain 'M' and resid 618 through 626 Processing helix chain 'M' and resid 627 through 636 Processing helix chain 'M' and resid 638 through 661 Processing helix chain 'N' and resid 58 through 64 removed outlier: 4.225A pdb=" N ASP N 63 " --> pdb=" O SER N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 79 Processing helix chain 'O' and resid 28 through 30 No H-bonds generated for 'chain 'O' and resid 28 through 30' Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 99 through 100C Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.736A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 197 through 202 Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 10.071A pdb=" N GLN A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N CYS A 296 " --> pdb=" O GLN A 442 " (cutoff:3.500A) removed outlier: 9.981A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.406A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.897A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.406A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.981A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N CYS A 296 " --> pdb=" O GLN A 442 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N GLN A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE A 359 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA9, first strand: chain 'L' and resid 11 through 12 removed outlier: 5.875A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 11 through 12 removed outlier: 5.875A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 2 through 5 removed outlier: 6.321A pdb=" N LYS C 2 " --> pdb=" O GLN C 94 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU C 96 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL C 4 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE C 26 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLY C 38 " --> pdb=" O PHE C 26 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TRP C 28 " --> pdb=" O ILE C 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 12 through 17 Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.619A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB7, first strand: chain 'D' and resid 35 through 40 Processing sheet with id=AB8, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.736A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AC2, first strand: chain 'D' and resid 197 through 202 Processing sheet with id=AC3, first strand: chain 'D' and resid 259 through 261 removed outlier: 10.071A pdb=" N GLN D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N CYS D 296 " --> pdb=" O GLN D 442 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.405A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER D 334 " --> pdb=" O GLU D 293 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.896A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.405A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N CYS D 296 " --> pdb=" O GLN D 442 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N GLN D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR D 467 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR D 357 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N PHE D 468 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE D 359 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AC6, first strand: chain 'E' and resid 11 through 12 removed outlier: 5.875A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 11 through 12 removed outlier: 5.875A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 2 through 5 removed outlier: 6.322A pdb=" N LYS G 2 " --> pdb=" O GLN G 94 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU G 96 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL G 4 " --> pdb=" O LEU G 96 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE G 26 " --> pdb=" O GLY G 38 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLY G 38 " --> pdb=" O PHE G 26 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TRP G 28 " --> pdb=" O ILE G 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 12 through 17 Processing sheet with id=AD1, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.619A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL I 56 " --> pdb=" O ILE I 52 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 10 through 12 Processing sheet with id=AD4, first strand: chain 'J' and resid 35 through 40 Processing sheet with id=AD5, first strand: chain 'J' and resid 45 through 47 removed outlier: 4.736A pdb=" N VAL J 242 " --> pdb=" O LEU J 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'J' and resid 91 through 92 Processing sheet with id=AD8, first strand: chain 'J' and resid 197 through 202 Processing sheet with id=AD9, first strand: chain 'J' and resid 259 through 261 removed outlier: 10.071A pdb=" N GLN J 442 " --> pdb=" O CYS J 296 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N CYS J 296 " --> pdb=" O GLN J 442 " (cutoff:3.500A) removed outlier: 9.981A pdb=" N ARG J 444 " --> pdb=" O ILE J 294 " (cutoff:3.500A) removed outlier: 11.406A pdb=" N ILE J 294 " --> pdb=" O ARG J 444 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N SER J 446 " --> pdb=" O VAL J 292 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N VAL J 292 " --> pdb=" O SER J 446 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N ASN J 448 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N GLU J 290 " --> pdb=" O ASN J 448 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR J 450 " --> pdb=" O LEU J 288 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLU J 293 " --> pdb=" O SER J 334 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER J 334 " --> pdb=" O GLU J 293 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 271 through 273 removed outlier: 6.896A pdb=" N THR J 450 " --> pdb=" O LEU J 288 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N GLU J 290 " --> pdb=" O ASN J 448 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N ASN J 448 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N VAL J 292 " --> pdb=" O SER J 446 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N SER J 446 " --> pdb=" O VAL J 292 " (cutoff:3.500A) removed outlier: 11.406A pdb=" N ILE J 294 " --> pdb=" O ARG J 444 " (cutoff:3.500A) removed outlier: 9.981A pdb=" N ARG J 444 " --> pdb=" O ILE J 294 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N CYS J 296 " --> pdb=" O GLN J 442 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N GLN J 442 " --> pdb=" O CYS J 296 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR J 467 " --> pdb=" O ASP J 457 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR J 357 " --> pdb=" O GLU J 466 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N PHE J 468 " --> pdb=" O THR J 357 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE J 359 " --> pdb=" O PHE J 468 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AE3, first strand: chain 'K' and resid 11 through 12 removed outlier: 5.875A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 11 through 12 removed outlier: 5.875A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 2 through 5 removed outlier: 6.321A pdb=" N LYS N 2 " --> pdb=" O GLN N 94 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU N 96 " --> pdb=" O LYS N 2 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL N 4 " --> pdb=" O LEU N 96 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE N 26 " --> pdb=" O GLY N 38 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLY N 38 " --> pdb=" O PHE N 26 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TRP N 28 " --> pdb=" O ILE N 36 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 12 through 17 Processing sheet with id=AE7, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'O' and resid 10 through 12 removed outlier: 3.619A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL O 56 " --> pdb=" O ILE O 52 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 10 through 12 897 hydrogen bonds defined for protein. 2223 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.37 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3968 1.31 - 1.44: 6065 1.44 - 1.58: 11648 1.58 - 1.71: 30 1.71 - 1.84: 144 Bond restraints: 21855 Sorted by residual: bond pdb=" C1 NAG D 624 " pdb=" O5 NAG D 624 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C1 NAG o 2 " pdb=" O5 NAG o 2 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.92e+01 ... (remaining 21850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 23756 2.03 - 4.07: 4785 4.07 - 6.10: 901 6.10 - 8.13: 168 8.13 - 10.17: 39 Bond angle restraints: 29649 Sorted by residual: angle pdb=" C PRO A 437 " pdb=" N PRO A 438 " pdb=" CA PRO A 438 " ideal model delta sigma weight residual 119.92 129.91 -9.99 1.07e+00 8.73e-01 8.72e+01 angle pdb=" C PRO J 437 " pdb=" N PRO J 438 " pdb=" CA PRO J 438 " ideal model delta sigma weight residual 119.92 129.91 -9.99 1.07e+00 8.73e-01 8.71e+01 angle pdb=" C PRO D 437 " pdb=" N PRO D 438 " pdb=" CA PRO D 438 " ideal model delta sigma weight residual 119.92 129.88 -9.96 1.07e+00 8.73e-01 8.66e+01 angle pdb=" C PHE D 353 " pdb=" N PRO D 354 " pdb=" CA PRO D 354 " ideal model delta sigma weight residual 119.56 127.41 -7.85 1.02e+00 9.61e-01 5.93e+01 angle pdb=" C PHE J 353 " pdb=" N PRO J 354 " pdb=" CA PRO J 354 " ideal model delta sigma weight residual 119.56 127.41 -7.85 1.02e+00 9.61e-01 5.92e+01 ... (remaining 29644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 11875 17.92 - 35.83: 350 35.83 - 53.74: 99 53.74 - 71.66: 57 71.66 - 89.57: 12 Dihedral angle restraints: 12393 sinusoidal: 5031 harmonic: 7362 Sorted by residual: dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -161.69 75.69 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CB CYS D 119 " pdb=" SG CYS D 119 " pdb=" SG CYS D 205 " pdb=" CB CYS D 205 " ideal model delta sinusoidal sigma weight residual -86.00 -161.69 75.69 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CB CYS J 119 " pdb=" SG CYS J 119 " pdb=" SG CYS J 205 " pdb=" CB CYS J 205 " ideal model delta sinusoidal sigma weight residual -86.00 -161.67 75.67 1 1.00e+01 1.00e-02 7.22e+01 ... (remaining 12390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 2811 0.118 - 0.235: 698 0.235 - 0.353: 68 0.353 - 0.470: 14 0.470 - 0.588: 6 Chirality restraints: 3597 Sorted by residual: chirality pdb=" C1 BMA R 3 " pdb=" O4 NAG R 2 " pdb=" C2 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 BMA l 3 " pdb=" O4 NAG l 2 " pdb=" C2 BMA l 3 " pdb=" O5 BMA l 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 chirality pdb=" C1 BMA b 3 " pdb=" O4 NAG b 2 " pdb=" C2 BMA b 3 " pdb=" O5 BMA b 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.11e+02 ... (remaining 3594 not shown) Planarity restraints: 3708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG p 1 " -0.059 2.00e-02 2.50e+03 4.85e-02 2.94e+01 pdb=" C7 NAG p 1 " 0.013 2.00e-02 2.50e+03 pdb=" C8 NAG p 1 " -0.044 2.00e-02 2.50e+03 pdb=" N2 NAG p 1 " 0.078 2.00e-02 2.50e+03 pdb=" O7 NAG p 1 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 1 " 0.059 2.00e-02 2.50e+03 4.84e-02 2.93e+01 pdb=" C7 NAG V 1 " -0.013 2.00e-02 2.50e+03 pdb=" C8 NAG V 1 " 0.044 2.00e-02 2.50e+03 pdb=" N2 NAG V 1 " -0.077 2.00e-02 2.50e+03 pdb=" O7 NAG V 1 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 1 " 0.059 2.00e-02 2.50e+03 4.82e-02 2.90e+01 pdb=" C7 NAG f 1 " -0.013 2.00e-02 2.50e+03 pdb=" C8 NAG f 1 " 0.044 2.00e-02 2.50e+03 pdb=" N2 NAG f 1 " -0.077 2.00e-02 2.50e+03 pdb=" O7 NAG f 1 " -0.012 2.00e-02 2.50e+03 ... (remaining 3705 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 8865 2.89 - 3.39: 18646 3.39 - 3.90: 36958 3.90 - 4.40: 41724 4.40 - 4.90: 68164 Nonbonded interactions: 174357 Sorted by model distance: nonbonded pdb=" N ASN D 88 " pdb=" OD1 ASN D 88 " model vdw 2.392 3.120 nonbonded pdb=" N ASN J 88 " pdb=" OD1 ASN J 88 " model vdw 2.392 3.120 nonbonded pdb=" N ASN A 88 " pdb=" OD1 ASN A 88 " model vdw 2.393 3.120 nonbonded pdb=" O5 NAG b 1 " pdb=" O6 NAG b 1 " model vdw 2.425 2.432 nonbonded pdb=" O5 NAG l 1 " pdb=" O6 NAG l 1 " model vdw 2.426 2.432 ... (remaining 174352 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' } ncs_group { reference = chain 'R' selection = chain 'b' selection = chain 'l' } ncs_group { reference = chain 'Y' selection = chain 'i' selection = chain 's' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.040 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 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 : 0.022 0.146 21984 Z= 1.173 Angle : 1.786 10.168 29997 Z= 1.137 Chirality : 0.103 0.588 3597 Planarity : 0.009 0.049 3660 Dihedral : 10.602 89.575 7530 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.79 % Favored : 97.97 % Rotamer: Outliers : 0.41 % Allowed : 0.27 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.16), residues: 2517 helix: 0.82 (0.23), residues: 438 sheet: 1.47 (0.20), residues: 663 loop : 0.45 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 542 TYR 0.036 0.008 TYR A 486 PHE 0.044 0.007 PHE E 98 TRP 0.055 0.011 TRP D 479 HIS 0.011 0.003 HIS J 374 Details of bonding type rmsd/Z covalent geometry : bond 0.02220 / 1.17 (21855) covalent geometry : angle 1.76177 / 1.14 (29649) SS BOND : bond 0.04666 / 3.23 ( 39) SS BOND : angle 3.08482 / 2.19 ( 78) hydrogen bonds : bond 0.16289 / 10.69 ( 855) hydrogen bonds : angle 7.49237 / 5.26 ( 2223) link_ALPHA1-2 : bond 0.03861 / 1.72 ( 3) link_ALPHA1-2 : angle 3.23613 / 1.98 ( 9) link_ALPHA1-3 : bond 0.03153 / 1.40 ( 3) link_ALPHA1-3 : angle 2.01406 / 1.22 ( 9) link_BETA1-4 : bond 0.02830 / 1.70 ( 36) link_BETA1-4 : angle 3.61962 / 2.46 ( 108) link_NAG-ASN : bond 0.02874 / 1.86 ( 48) link_NAG-ASN : angle 3.05076 / 2.17 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 642 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.7584 (t0) cc_final: 0.7298 (p0) REVERT: A 113 ASP cc_start: 0.7837 (m-30) cc_final: 0.7620 (m-30) REVERT: A 210 PHE cc_start: 0.8844 (t80) cc_final: 0.8619 (t80) REVERT: A 279 ASP cc_start: 0.7218 (p0) cc_final: 0.6614 (t0) REVERT: A 377 ASN cc_start: 0.8470 (t0) cc_final: 0.7680 (t0) REVERT: L 36 TYR cc_start: 0.6951 (m-80) cc_final: 0.6735 (m-80) REVERT: C 81 THR cc_start: 0.8697 (m) cc_final: 0.8218 (p) REVERT: H 27 ASP cc_start: 0.8064 (t0) cc_final: 0.7744 (t0) REVERT: H 100 TYR cc_start: 0.7196 (t80) cc_final: 0.6636 (t80) REVERT: H 100 ASP cc_start: 0.6086 (m-30) cc_final: 0.5754 (m-30) REVERT: D 80 ASN cc_start: 0.7900 (t0) cc_final: 0.7618 (p0) REVERT: D 95 MET cc_start: 0.8588 (ptm) cc_final: 0.8274 (ptp) REVERT: D 279 ASP cc_start: 0.6918 (p0) cc_final: 0.6157 (t0) REVERT: D 475 MET cc_start: 0.8362 (mmt) cc_final: 0.8098 (mmt) REVERT: F 617 LYS cc_start: 0.8629 (mttm) cc_final: 0.8283 (mtmt) REVERT: F 634 GLU cc_start: 0.8128 (tp30) cc_final: 0.7804 (tp30) REVERT: I 12 LYS cc_start: 0.8006 (mmtt) cc_final: 0.7771 (mtpt) REVERT: I 82 LEU cc_start: 0.7751 (tp) cc_final: 0.7534 (tp) REVERT: I 87 THR cc_start: 0.7866 (m) cc_final: 0.7635 (t) REVERT: I 100 TYR cc_start: 0.7485 (t80) cc_final: 0.6387 (t80) REVERT: I 100 ASP cc_start: 0.5980 (m-30) cc_final: 0.5466 (m-30) REVERT: I 100 ASN cc_start: 0.6613 (t0) cc_final: 0.6357 (t0) REVERT: J 279 ASP cc_start: 0.7098 (p0) cc_final: 0.6319 (t0) REVERT: M 620 ASN cc_start: 0.7993 (m-40) cc_final: 0.7721 (m-40) REVERT: N 5 LEU cc_start: 0.8486 (tt) cc_final: 0.8246 (tt) REVERT: O 12 LYS cc_start: 0.7936 (mmtt) cc_final: 0.7669 (mtpt) REVERT: O 19 LYS cc_start: 0.7362 (tttt) cc_final: 0.7112 (mmtt) REVERT: O 27 ASP cc_start: 0.8128 (t0) cc_final: 0.7722 (t0) REVERT: O 82 LEU cc_start: 0.7798 (tp) cc_final: 0.7587 (tp) REVERT: O 100 TYR cc_start: 0.7244 (t80) cc_final: 0.6245 (t80) REVERT: O 100 ASN cc_start: 0.6568 (t0) cc_final: 0.6290 (t0) outliers start: 9 outliers final: 2 residues processed: 648 average time/residue: 0.1748 time to fit residues: 168.2618 Evaluate side-chains 342 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 340 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain J residue 88 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN A 422 GLN L 89 GLN B 575 GLN B 607 ASN H 102 HIS D 72 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 1 GLN I 102 HIS ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 575 GLN M 607 ASN M 652 GLN ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.131683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.102625 restraints weight = 35273.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.105466 restraints weight = 25205.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.106421 restraints weight = 17398.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.107734 restraints weight = 15369.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.107804 restraints weight = 13979.376| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21984 Z= 0.188 Angle : 0.780 21.252 29997 Z= 0.400 Chirality : 0.048 0.269 3597 Planarity : 0.005 0.042 3660 Dihedral : 5.763 43.583 2767 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.35 % Allowed : 8.57 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.16), residues: 2517 helix: 1.83 (0.24), residues: 435 sheet: 1.17 (0.20), residues: 654 loop : -0.24 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 337 TYR 0.023 0.002 TYR I 32 PHE 0.022 0.003 PHE L 98 TRP 0.017 0.002 TRP M 614 HIS 0.005 0.001 HIS J 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (21855) covalent geometry : angle 0.73096 / 0.39 (29649) SS BOND : bond 0.00417 / 0.24 ( 39) SS BOND : angle 1.42672 / 0.96 ( 78) hydrogen bonds : bond 0.05697 / 3.78 ( 855) hydrogen bonds : angle 5.92486 / 4.11 ( 2223) link_ALPHA1-2 : bond 0.00009 / 0.00 ( 3) link_ALPHA1-2 : angle 1.82398 / 1.03 ( 9) link_ALPHA1-3 : bond 0.00132 / 0.05 ( 3) link_ALPHA1-3 : angle 1.52148 / 0.87 ( 9) link_BETA1-4 : bond 0.00431 / 0.27 ( 36) link_BETA1-4 : angle 1.90757 / 1.27 ( 108) link_NAG-ASN : bond 0.00412 / 0.28 ( 48) link_NAG-ASN : angle 3.56375 / 2.33 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 405 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.5405 (m) cc_final: 0.4973 (m) REVERT: A 80 ASN cc_start: 0.7759 (t0) cc_final: 0.7418 (p0) REVERT: A 210 PHE cc_start: 0.8780 (t80) cc_final: 0.8558 (t80) REVERT: A 305 LYS cc_start: 0.5639 (mmtp) cc_final: 0.5209 (mmtt) REVERT: A 341 THR cc_start: 0.8513 (m) cc_final: 0.8189 (p) REVERT: L 78 LEU cc_start: 0.7940 (tp) cc_final: 0.7461 (tt) REVERT: L 92 ASN cc_start: 0.8298 (t0) cc_final: 0.7840 (t0) REVERT: L 95 ARG cc_start: 0.6997 (ptp-110) cc_final: 0.6490 (mtt90) REVERT: B 518 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.5856 (t80) REVERT: B 543 LEU cc_start: 0.8559 (mp) cc_final: 0.8329 (tp) REVERT: H 12 LYS cc_start: 0.7698 (mtpt) cc_final: 0.7430 (mtpt) REVERT: D 74 CYS cc_start: 0.5183 (m) cc_final: 0.4847 (m) REVERT: D 80 ASN cc_start: 0.7945 (t0) cc_final: 0.7732 (p0) REVERT: D 95 MET cc_start: 0.8520 (ptm) cc_final: 0.8194 (ptp) REVERT: D 104 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8125 (ttm) REVERT: D 252 ARG cc_start: 0.8522 (mtt90) cc_final: 0.8235 (mtt-85) REVERT: E 49 TYR cc_start: 0.5548 (OUTLIER) cc_final: 0.5299 (t80) REVERT: F 518 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.6147 (t80) REVERT: F 617 LYS cc_start: 0.8714 (mttm) cc_final: 0.8384 (mtmt) REVERT: F 636 ASP cc_start: 0.8469 (t0) cc_final: 0.8188 (t0) REVERT: G 12 VAL cc_start: 0.8609 (t) cc_final: 0.8269 (p) REVERT: G 94 GLN cc_start: 0.8503 (tt0) cc_final: 0.8070 (tm-30) REVERT: J 40 TYR cc_start: 0.8881 (t80) cc_final: 0.8568 (t80) REVERT: J 74 CYS cc_start: 0.5354 (m) cc_final: 0.5078 (m) REVERT: J 399 THR cc_start: 0.7405 (p) cc_final: 0.7168 (t) REVERT: K 91 TYR cc_start: 0.3884 (m-80) cc_final: 0.3001 (m-10) REVERT: M 518 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.5928 (t80) REVERT: M 542 ARG cc_start: 0.7295 (mtm-85) cc_final: 0.6994 (mtt90) REVERT: M 620 ASN cc_start: 0.8092 (m-40) cc_final: 0.7829 (m-40) REVERT: O 19 LYS cc_start: 0.7711 (tttt) cc_final: 0.7310 (mmtt) REVERT: O 82 LEU cc_start: 0.7796 (tp) cc_final: 0.7533 (tp) REVERT: O 100 TYR cc_start: 0.6615 (t80) cc_final: 0.5769 (t80) REVERT: O 100 ASN cc_start: 0.6353 (t0) cc_final: 0.6050 (t0) REVERT: O 100 PHE cc_start: 0.7056 (p90) cc_final: 0.6837 (p90) outliers start: 52 outliers final: 23 residues processed: 438 average time/residue: 0.1729 time to fit residues: 112.4723 Evaluate side-chains 354 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 326 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain F residue 518 PHE Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain M residue 518 PHE Chi-restraints excluded: chain M residue 607 ASN Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 79 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 9 optimal weight: 0.9980 chunk 177 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 231 optimal weight: 0.9990 chunk 170 optimal weight: 0.0030 chunk 189 optimal weight: 0.1980 chunk 128 optimal weight: 5.9990 chunk 175 optimal weight: 0.0020 chunk 46 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 221 optimal weight: 0.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN B 607 ASN D 280 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 1 GLN K 100 GLN M 607 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.134196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.106637 restraints weight = 34912.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.109077 restraints weight = 28059.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.110124 restraints weight = 20786.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.110856 restraints weight = 17229.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.111116 restraints weight = 15940.063| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21984 Z= 0.130 Angle : 0.644 10.464 29997 Z= 0.331 Chirality : 0.044 0.205 3597 Planarity : 0.004 0.043 3660 Dihedral : 5.338 45.998 2765 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.85 % Allowed : 9.88 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.17), residues: 2517 helix: 2.02 (0.25), residues: 435 sheet: 0.94 (0.20), residues: 639 loop : -0.30 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 542 TYR 0.021 0.002 TYR E 49 PHE 0.017 0.002 PHE E 83 TRP 0.013 0.001 TRP M 571 HIS 0.007 0.001 HIS H 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (21855) covalent geometry : angle 0.61427 / 0.33 (29649) SS BOND : bond 0.00251 / 0.14 ( 39) SS BOND : angle 0.84332 / 0.54 ( 78) hydrogen bonds : bond 0.04592 / 3.04 ( 855) hydrogen bonds : angle 5.54233 / 3.82 ( 2223) link_ALPHA1-2 : bond 0.00138 / 0.07 ( 3) link_ALPHA1-2 : angle 1.67847 / 0.96 ( 9) link_ALPHA1-3 : bond 0.01005 / 0.47 ( 3) link_ALPHA1-3 : angle 1.20154 / 0.68 ( 9) link_BETA1-4 : bond 0.00430 / 0.27 ( 36) link_BETA1-4 : angle 1.38773 / 0.92 ( 108) link_NAG-ASN : bond 0.00489 / 0.35 ( 48) link_NAG-ASN : angle 2.55954 / 1.71 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 390 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.7803 (ttm) REVERT: A 341 THR cc_start: 0.8503 (m) cc_final: 0.8296 (p) REVERT: A 499 THR cc_start: 0.8841 (m) cc_final: 0.8625 (m) REVERT: L 78 LEU cc_start: 0.8122 (tp) cc_final: 0.7835 (tt) REVERT: L 95 ARG cc_start: 0.6895 (ptp-110) cc_final: 0.6581 (mtt90) REVERT: H 28 THR cc_start: 0.8149 (p) cc_final: 0.7614 (p) REVERT: H 89 VAL cc_start: 0.7621 (OUTLIER) cc_final: 0.7396 (m) REVERT: D 95 MET cc_start: 0.8100 (ptm) cc_final: 0.7799 (ptp) REVERT: F 519 ILE cc_start: 0.8489 (mt) cc_final: 0.8080 (mt) REVERT: F 636 ASP cc_start: 0.8035 (t0) cc_final: 0.7779 (t0) REVERT: J 40 TYR cc_start: 0.8931 (t80) cc_final: 0.8646 (t80) REVERT: J 80 ASN cc_start: 0.7516 (p0) cc_final: 0.7271 (p0) REVERT: K 89 GLN cc_start: 0.6926 (tt0) cc_final: 0.6656 (pt0) REVERT: M 620 ASN cc_start: 0.7346 (m-40) cc_final: 0.7031 (m-40) REVERT: M 659 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7571 (tm-30) REVERT: O 12 LYS cc_start: 0.7836 (mmtt) cc_final: 0.7537 (mmmm) REVERT: O 66 ARG cc_start: 0.7315 (mtp180) cc_final: 0.6907 (mtp180) REVERT: O 82 LEU cc_start: 0.7675 (tp) cc_final: 0.7440 (tp) REVERT: O 100 TYR cc_start: 0.6943 (t80) cc_final: 0.6312 (t80) outliers start: 41 outliers final: 17 residues processed: 412 average time/residue: 0.1665 time to fit residues: 103.3945 Evaluate side-chains 325 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 306 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 10 GLU Chi-restraints excluded: chain O residue 17 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 100 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 230 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 163 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 280 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN L 100 GLN H 1 GLN D 66 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN J 66 HIS J 422 GLN K 100 GLN M 540 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.123882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.097237 restraints weight = 35616.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.097808 restraints weight = 30186.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.098912 restraints weight = 26679.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.099333 restraints weight = 22550.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.099555 restraints weight = 21382.955| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.056 21984 Z= 0.359 Angle : 0.821 7.630 29997 Z= 0.422 Chirality : 0.051 0.179 3597 Planarity : 0.005 0.057 3660 Dihedral : 6.361 59.092 2763 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.29 % Allowed : 11.32 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.16), residues: 2517 helix: 1.81 (0.25), residues: 420 sheet: 0.44 (0.20), residues: 654 loop : -0.95 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 83 TYR 0.022 0.003 TYR A 484 PHE 0.024 0.003 PHE J 376 TRP 0.023 0.003 TRP A 45 HIS 0.017 0.002 HIS J 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00855 / 0.36 (21855) covalent geometry : angle 0.79900 / 0.42 (29649) SS BOND : bond 0.00482 / 0.29 ( 39) SS BOND : angle 1.31810 / 0.91 ( 78) hydrogen bonds : bond 0.05719 / 3.79 ( 855) hydrogen bonds : angle 5.80054 / 4.04 ( 2223) link_ALPHA1-2 : bond 0.00603 / 0.26 ( 3) link_ALPHA1-2 : angle 2.35542 / 1.37 ( 9) link_ALPHA1-3 : bond 0.00545 / 0.25 ( 3) link_ALPHA1-3 : angle 1.52909 / 0.87 ( 9) link_BETA1-4 : bond 0.00398 / 0.24 ( 36) link_BETA1-4 : angle 1.59258 / 1.07 ( 108) link_NAG-ASN : bond 0.00463 / 0.28 ( 48) link_NAG-ASN : angle 2.38524 / 1.68 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 361 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7771 (ttm) REVERT: A 377 ASN cc_start: 0.7946 (t0) cc_final: 0.7588 (t0) REVERT: A 462 GLN cc_start: 0.6937 (mm110) cc_final: 0.6437 (mm110) REVERT: A 475 MET cc_start: 0.7787 (mmt) cc_final: 0.7516 (mmt) REVERT: L 78 LEU cc_start: 0.8446 (tp) cc_final: 0.8241 (tt) REVERT: L 92 ASN cc_start: 0.8118 (t0) cc_final: 0.7770 (t0) REVERT: H 66 ARG cc_start: 0.7151 (mtp180) cc_final: 0.6845 (ttp-170) REVERT: H 99 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6856 (mm-30) REVERT: D 279 ASP cc_start: 0.7534 (t0) cc_final: 0.7321 (t0) REVERT: D 404 TYR cc_start: 0.7780 (m-80) cc_final: 0.7577 (m-80) REVERT: D 434 MET cc_start: 0.7762 (ttt) cc_final: 0.7098 (ttt) REVERT: E 49 TYR cc_start: 0.5010 (OUTLIER) cc_final: 0.4584 (t80) REVERT: I 100 TYR cc_start: 0.7737 (t80) cc_final: 0.6392 (t80) REVERT: J 80 ASN cc_start: 0.7798 (p0) cc_final: 0.7459 (p0) REVERT: K 92 ASN cc_start: 0.8284 (t0) cc_final: 0.7809 (t0) REVERT: M 620 ASN cc_start: 0.7488 (m-40) cc_final: 0.7089 (m-40) REVERT: M 655 LYS cc_start: 0.8545 (ttpp) cc_final: 0.8295 (ttmm) REVERT: O 100 TYR cc_start: 0.7470 (t80) cc_final: 0.6958 (t80) outliers start: 73 outliers final: 50 residues processed: 409 average time/residue: 0.1678 time to fit residues: 103.8961 Evaluate side-chains 353 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 301 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 518 PHE Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain M residue 518 PHE Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 546 SER Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain M residue 589 ASP Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 179 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 186 optimal weight: 0.9990 chunk 219 optimal weight: 0.7980 chunk 216 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN I 1 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.127886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.100973 restraints weight = 35036.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.102002 restraints weight = 29149.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.103008 restraints weight = 25270.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.103514 restraints weight = 20701.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.104122 restraints weight = 19305.596| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21984 Z= 0.155 Angle : 0.659 11.540 29997 Z= 0.336 Chirality : 0.046 0.242 3597 Planarity : 0.004 0.049 3660 Dihedral : 6.024 59.995 2763 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.17 % Allowed : 13.53 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.17), residues: 2517 helix: 2.01 (0.26), residues: 432 sheet: 0.66 (0.20), residues: 642 loop : -0.92 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 54 TYR 0.018 0.002 TYR L 91 PHE 0.015 0.002 PHE O 91 TRP 0.025 0.002 TRP K 35 HIS 0.007 0.001 HIS H 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (21855) covalent geometry : angle 0.62960 / 0.33 (29649) SS BOND : bond 0.00296 / 0.20 ( 39) SS BOND : angle 1.69788 / 1.28 ( 78) hydrogen bonds : bond 0.04537 / 2.99 ( 855) hydrogen bonds : angle 5.43696 / 3.76 ( 2223) link_ALPHA1-2 : bond 0.00032 / 0.01 ( 3) link_ALPHA1-2 : angle 1.88679 / 1.09 ( 9) link_ALPHA1-3 : bond 0.00684 / 0.30 ( 3) link_ALPHA1-3 : angle 1.16205 / 0.66 ( 9) link_BETA1-4 : bond 0.00328 / 0.20 ( 36) link_BETA1-4 : angle 1.24795 / 0.83 ( 108) link_NAG-ASN : bond 0.00559 / 0.40 ( 48) link_NAG-ASN : angle 2.43573 / 1.62 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 354 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7917 (ttm) REVERT: A 280 ASN cc_start: 0.6928 (OUTLIER) cc_final: 0.6460 (t0) REVERT: A 377 ASN cc_start: 0.7919 (t0) cc_final: 0.7546 (t0) REVERT: A 462 GLN cc_start: 0.7050 (mm110) cc_final: 0.6401 (mm110) REVERT: A 475 MET cc_start: 0.7400 (mmt) cc_final: 0.7136 (mmt) REVERT: L 78 LEU cc_start: 0.8201 (tp) cc_final: 0.7911 (tt) REVERT: L 92 ASN cc_start: 0.8413 (t0) cc_final: 0.8187 (t0) REVERT: E 24 ARG cc_start: 0.7102 (ttm110) cc_final: 0.6890 (ttm110) REVERT: G 73 ASN cc_start: 0.8792 (t0) cc_final: 0.8555 (t0) REVERT: J 80 ASN cc_start: 0.7768 (p0) cc_final: 0.7382 (p0) REVERT: M 620 ASN cc_start: 0.7505 (m-40) cc_final: 0.7148 (m-40) REVERT: M 655 LYS cc_start: 0.8545 (ttpp) cc_final: 0.8258 (ttmm) REVERT: O 1 GLN cc_start: 0.7538 (mp10) cc_final: 0.7019 (mp10) REVERT: O 17 SER cc_start: 0.6675 (OUTLIER) cc_final: 0.5490 (m) REVERT: O 100 TYR cc_start: 0.7299 (t80) cc_final: 0.6923 (t80) outliers start: 48 outliers final: 32 residues processed: 386 average time/residue: 0.1730 time to fit residues: 100.3380 Evaluate side-chains 349 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 314 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain J residue 402 ASP Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 589 ASP Chi-restraints excluded: chain M residue 612 ASP Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 10 GLU Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 84 optimal weight: 0.8980 chunk 220 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 28 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 199 optimal weight: 4.9990 chunk 137 optimal weight: 0.5980 chunk 124 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 1 GLN J 72 HIS K 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.129086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101992 restraints weight = 35027.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.103648 restraints weight = 28576.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.104194 restraints weight = 23431.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104887 restraints weight = 20650.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.105270 restraints weight = 18107.454| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21984 Z= 0.136 Angle : 0.634 10.948 29997 Z= 0.326 Chirality : 0.045 0.224 3597 Planarity : 0.004 0.047 3660 Dihedral : 5.817 59.210 2763 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.35 % Allowed : 14.48 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.17), residues: 2517 helix: 2.16 (0.26), residues: 432 sheet: 0.54 (0.20), residues: 660 loop : -0.86 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 54 TYR 0.022 0.001 TYR L 91 PHE 0.018 0.002 PHE H 100J TRP 0.027 0.001 TRP L 35 HIS 0.007 0.001 HIS I 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (21855) covalent geometry : angle 0.60814 / 0.32 (29649) SS BOND : bond 0.00458 / 0.21 ( 39) SS BOND : angle 2.16103 / 1.65 ( 78) hydrogen bonds : bond 0.04187 / 2.76 ( 855) hydrogen bonds : angle 5.35076 / 3.71 ( 2223) link_ALPHA1-2 : bond 0.00379 / 0.18 ( 3) link_ALPHA1-2 : angle 1.79789 / 1.04 ( 9) link_ALPHA1-3 : bond 0.00570 / 0.25 ( 3) link_ALPHA1-3 : angle 1.09971 / 0.63 ( 9) link_BETA1-4 : bond 0.00305 / 0.19 ( 36) link_BETA1-4 : angle 1.19772 / 0.80 ( 108) link_NAG-ASN : bond 0.00168 / 0.09 ( 48) link_NAG-ASN : angle 1.91149 / 1.33 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 345 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7939 (ttm) REVERT: A 377 ASN cc_start: 0.7926 (t0) cc_final: 0.7687 (t0) REVERT: A 462 GLN cc_start: 0.6895 (mm110) cc_final: 0.6318 (mm110) REVERT: A 475 MET cc_start: 0.7350 (mmt) cc_final: 0.7064 (mmt) REVERT: B 542 ARG cc_start: 0.8547 (ttp-110) cc_final: 0.7950 (mtm-85) REVERT: D 104 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7662 (ttm) REVERT: D 403 ASP cc_start: 0.8216 (m-30) cc_final: 0.7934 (m-30) REVERT: E 24 ARG cc_start: 0.7078 (ttm110) cc_final: 0.6855 (ttm110) REVERT: E 33 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7908 (tp) REVERT: J 80 ASN cc_start: 0.7738 (p0) cc_final: 0.7373 (p0) REVERT: J 462 GLN cc_start: 0.6377 (mm-40) cc_final: 0.5941 (mm-40) REVERT: M 620 ASN cc_start: 0.7533 (m-40) cc_final: 0.7197 (m-40) REVERT: M 655 LYS cc_start: 0.8521 (ttpp) cc_final: 0.8234 (ttmm) REVERT: O 1 GLN cc_start: 0.7520 (mp10) cc_final: 0.6954 (mp10) REVERT: O 12 LYS cc_start: 0.7545 (mmmt) cc_final: 0.7017 (mmmt) REVERT: O 100 TYR cc_start: 0.7324 (t80) cc_final: 0.6953 (t80) outliers start: 52 outliers final: 31 residues processed: 380 average time/residue: 0.1706 time to fit residues: 97.6735 Evaluate side-chains 345 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 311 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain M residue 589 ASP Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 19 SER Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 101 LYS Chi-restraints excluded: chain O residue 108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 103 optimal weight: 7.9990 chunk 195 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 91 optimal weight: 0.0870 chunk 83 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 HIS ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.126249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.099636 restraints weight = 35216.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.100311 restraints weight = 29882.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.101310 restraints weight = 26248.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.101867 restraints weight = 22327.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.102694 restraints weight = 21192.970| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 21984 Z= 0.226 Angle : 0.709 9.923 29997 Z= 0.361 Chirality : 0.047 0.279 3597 Planarity : 0.005 0.050 3660 Dihedral : 5.903 59.602 2763 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.44 % Allowed : 15.16 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.16), residues: 2517 helix: 1.74 (0.25), residues: 456 sheet: 0.57 (0.20), residues: 642 loop : -1.11 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 83 TYR 0.019 0.002 TYR O 79 PHE 0.017 0.002 PHE J 376 TRP 0.014 0.002 TRP D 479 HIS 0.041 0.002 HIS J 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (21855) covalent geometry : angle 0.68000 / 0.35 (29649) SS BOND : bond 0.00362 / 0.23 ( 39) SS BOND : angle 1.94739 / 1.46 ( 78) hydrogen bonds : bond 0.04637 / 3.06 ( 855) hydrogen bonds : angle 5.43962 / 3.79 ( 2223) link_ALPHA1-2 : bond 0.00185 / 0.08 ( 3) link_ALPHA1-2 : angle 2.12385 / 1.23 ( 9) link_ALPHA1-3 : bond 0.00684 / 0.31 ( 3) link_ALPHA1-3 : angle 1.25382 / 0.71 ( 9) link_BETA1-4 : bond 0.00293 / 0.18 ( 36) link_BETA1-4 : angle 1.32047 / 0.88 ( 108) link_NAG-ASN : bond 0.00404 / 0.26 ( 48) link_NAG-ASN : angle 2.37775 / 1.60 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 332 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8016 (ttm) REVERT: A 377 ASN cc_start: 0.7888 (t0) cc_final: 0.7647 (t0) REVERT: A 475 MET cc_start: 0.7540 (mmt) cc_final: 0.7229 (mmt) REVERT: L 79 GLN cc_start: 0.7676 (mp10) cc_final: 0.6720 (mp10) REVERT: B 542 ARG cc_start: 0.8298 (ttp-110) cc_final: 0.8004 (mtm-85) REVERT: D 402 ASP cc_start: 0.6776 (OUTLIER) cc_final: 0.6574 (p0) REVERT: E 79 GLN cc_start: 0.7888 (mp10) cc_final: 0.7245 (mp10) REVERT: G 5 LEU cc_start: 0.8330 (tp) cc_final: 0.8111 (tt) REVERT: J 80 ASN cc_start: 0.7665 (p0) cc_final: 0.7247 (p0) REVERT: K 54 ARG cc_start: 0.7594 (mtp85) cc_final: 0.7089 (mtp85) REVERT: M 544 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8625 (mt) REVERT: M 620 ASN cc_start: 0.7361 (m-40) cc_final: 0.7098 (m-40) REVERT: M 655 LYS cc_start: 0.8534 (ttpp) cc_final: 0.8257 (ttmm) REVERT: O 1 GLN cc_start: 0.7374 (mp10) cc_final: 0.6852 (mp10) REVERT: O 100 TYR cc_start: 0.7479 (t80) cc_final: 0.7085 (t80) outliers start: 54 outliers final: 40 residues processed: 365 average time/residue: 0.1800 time to fit residues: 97.8045 Evaluate side-chains 357 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 314 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 518 PHE Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 443 ILE Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain M residue 518 PHE Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 544 LEU Chi-restraints excluded: chain M residue 566 LEU Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain M residue 589 ASP Chi-restraints excluded: chain M residue 615 SER Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 19 SER Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 30 optimal weight: 0.8980 chunk 126 optimal weight: 0.0870 chunk 123 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 111 optimal weight: 0.0170 chunk 168 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 HIS K 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.129576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.103853 restraints weight = 34901.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.104897 restraints weight = 32303.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.106078 restraints weight = 28232.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.106455 restraints weight = 22980.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106746 restraints weight = 22275.858| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21984 Z= 0.123 Angle : 0.637 9.454 29997 Z= 0.326 Chirality : 0.045 0.361 3597 Planarity : 0.004 0.063 3660 Dihedral : 5.658 59.654 2763 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.17 % Allowed : 15.61 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.17), residues: 2517 helix: 1.98 (0.26), residues: 456 sheet: 0.67 (0.21), residues: 627 loop : -0.97 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 83 TYR 0.018 0.001 TYR K 91 PHE 0.035 0.002 PHE H 29 TRP 0.015 0.001 TRP M 571 HIS 0.031 0.001 HIS J 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (21855) covalent geometry : angle 0.61129 / 0.32 (29649) SS BOND : bond 0.00295 / 0.20 ( 39) SS BOND : angle 1.64353 / 1.23 ( 78) hydrogen bonds : bond 0.04000 / 2.62 ( 855) hydrogen bonds : angle 5.30231 / 3.68 ( 2223) link_ALPHA1-2 : bond 0.00065 / 0.03 ( 3) link_ALPHA1-2 : angle 1.83017 / 1.05 ( 9) link_ALPHA1-3 : bond 0.00699 / 0.31 ( 3) link_ALPHA1-3 : angle 1.15952 / 0.65 ( 9) link_BETA1-4 : bond 0.00345 / 0.21 ( 36) link_BETA1-4 : angle 1.16542 / 0.78 ( 108) link_NAG-ASN : bond 0.00296 / 0.21 ( 48) link_NAG-ASN : angle 2.22215 / 1.45 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 336 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7831 (ttm) REVERT: A 475 MET cc_start: 0.7217 (mmt) cc_final: 0.6966 (mmt) REVERT: L 79 GLN cc_start: 0.7645 (mp10) cc_final: 0.7284 (mt0) REVERT: B 542 ARG cc_start: 0.8167 (ttp-110) cc_final: 0.7937 (mtm-85) REVERT: D 104 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7598 (ttm) REVERT: E 79 GLN cc_start: 0.7939 (mp10) cc_final: 0.7305 (mp10) REVERT: J 80 ASN cc_start: 0.7501 (p0) cc_final: 0.7068 (p0) REVERT: K 78 LEU cc_start: 0.8044 (tp) cc_final: 0.7585 (tt) REVERT: M 544 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8577 (mt) REVERT: M 620 ASN cc_start: 0.7158 (m-40) cc_final: 0.6945 (m-40) REVERT: O 1 GLN cc_start: 0.7394 (mp10) cc_final: 0.6943 (mp10) REVERT: O 66 ARG cc_start: 0.6898 (mtp180) cc_final: 0.6678 (mtp180) REVERT: O 82 ARG cc_start: 0.6622 (OUTLIER) cc_final: 0.6382 (ptp90) REVERT: O 100 TYR cc_start: 0.7401 (t80) cc_final: 0.7078 (t80) outliers start: 48 outliers final: 32 residues processed: 367 average time/residue: 0.1691 time to fit residues: 92.3809 Evaluate side-chains 347 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 311 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 443 ILE Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 544 LEU Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain M residue 589 ASP Chi-restraints excluded: chain M residue 606 THR Chi-restraints excluded: chain M residue 615 SER Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 19 SER Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 82 ARG Chi-restraints excluded: chain O residue 108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 79 optimal weight: 7.9990 chunk 10 optimal weight: 0.4980 chunk 216 optimal weight: 6.9990 chunk 246 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN L 100 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN K 89 GLN M 630 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.126654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.100605 restraints weight = 35087.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.101077 restraints weight = 29421.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.101658 restraints weight = 26917.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.102535 restraints weight = 23135.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.103847 restraints weight = 21398.988| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 21984 Z= 0.204 Angle : 0.692 10.539 29997 Z= 0.354 Chirality : 0.047 0.264 3597 Planarity : 0.005 0.062 3660 Dihedral : 5.728 59.411 2763 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.30 % Allowed : 15.97 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.17), residues: 2517 helix: 1.86 (0.26), residues: 456 sheet: 0.38 (0.20), residues: 672 loop : -1.13 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 103 TYR 0.020 0.002 TYR H 79 PHE 0.034 0.002 PHE H 29 TRP 0.013 0.002 TRP M 571 HIS 0.010 0.001 HIS J 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 (21855) covalent geometry : angle 0.66573 / 0.35 (29649) SS BOND : bond 0.00393 / 0.23 ( 39) SS BOND : angle 1.96219 / 1.45 ( 78) hydrogen bonds : bond 0.04430 / 2.91 ( 855) hydrogen bonds : angle 5.39735 / 3.76 ( 2223) link_ALPHA1-2 : bond 0.00240 / 0.10 ( 3) link_ALPHA1-2 : angle 2.00048 / 1.16 ( 9) link_ALPHA1-3 : bond 0.00612 / 0.27 ( 3) link_ALPHA1-3 : angle 1.20461 / 0.68 ( 9) link_BETA1-4 : bond 0.00282 / 0.18 ( 36) link_BETA1-4 : angle 1.28882 / 0.86 ( 108) link_NAG-ASN : bond 0.00252 / 0.16 ( 48) link_NAG-ASN : angle 2.21486 / 1.49 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 320 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8019 (ttm) REVERT: A 475 MET cc_start: 0.7514 (mmt) cc_final: 0.7169 (mmt) REVERT: L 79 GLN cc_start: 0.7592 (mp10) cc_final: 0.7162 (mt0) REVERT: L 92 ASN cc_start: 0.8236 (t0) cc_final: 0.7933 (t0) REVERT: B 542 ARG cc_start: 0.8260 (ttp-110) cc_final: 0.8037 (mtm-85) REVERT: H 13 LYS cc_start: 0.7881 (mmtm) cc_final: 0.7376 (mptt) REVERT: D 104 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7650 (ttm) REVERT: J 80 ASN cc_start: 0.7509 (p0) cc_final: 0.7288 (p0) REVERT: K 92 ASN cc_start: 0.8268 (t0) cc_final: 0.7730 (t0) REVERT: M 544 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8625 (mt) REVERT: M 620 ASN cc_start: 0.7463 (m-40) cc_final: 0.7255 (m-40) REVERT: M 655 LYS cc_start: 0.8472 (ttpp) cc_final: 0.8184 (ttmm) REVERT: O 1 GLN cc_start: 0.7417 (mp10) cc_final: 0.6970 (mp10) REVERT: O 82 ARG cc_start: 0.6920 (ptp90) cc_final: 0.6241 (ptp90) REVERT: O 100 TYR cc_start: 0.7434 (t80) cc_final: 0.7002 (t80) outliers start: 51 outliers final: 41 residues processed: 351 average time/residue: 0.1696 time to fit residues: 88.2933 Evaluate side-chains 359 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 315 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 443 ILE Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 544 LEU Chi-restraints excluded: chain M residue 566 LEU Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain M residue 589 ASP Chi-restraints excluded: chain M residue 606 THR Chi-restraints excluded: chain M residue 615 SER Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 19 SER Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 235 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 241 optimal weight: 3.9990 chunk 226 optimal weight: 0.6980 chunk 49 optimal weight: 0.0050 chunk 117 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 232 optimal weight: 0.7980 chunk 169 optimal weight: 6.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.129145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.102391 restraints weight = 34965.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.104229 restraints weight = 27904.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.105095 restraints weight = 22604.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.105630 restraints weight = 19442.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.106188 restraints weight = 18403.167| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21984 Z= 0.135 Angle : 0.651 9.173 29997 Z= 0.333 Chirality : 0.045 0.273 3597 Planarity : 0.004 0.045 3660 Dihedral : 5.578 59.523 2763 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.03 % Allowed : 16.01 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.17), residues: 2517 helix: 1.99 (0.26), residues: 456 sheet: 0.46 (0.21), residues: 657 loop : -1.00 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 83 TYR 0.020 0.001 TYR K 91 PHE 0.033 0.002 PHE H 29 TRP 0.015 0.001 TRP M 571 HIS 0.007 0.001 HIS O 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (21855) covalent geometry : angle 0.62857 / 0.33 (29649) SS BOND : bond 0.00322 / 0.19 ( 39) SS BOND : angle 1.71456 / 1.30 ( 78) hydrogen bonds : bond 0.04024 / 2.62 ( 855) hydrogen bonds : angle 5.28891 / 3.67 ( 2223) link_ALPHA1-2 : bond 0.00132 / 0.06 ( 3) link_ALPHA1-2 : angle 1.80959 / 1.05 ( 9) link_ALPHA1-3 : bond 0.00644 / 0.28 ( 3) link_ALPHA1-3 : angle 1.19003 / 0.67 ( 9) link_BETA1-4 : bond 0.00330 / 0.20 ( 36) link_BETA1-4 : angle 1.17279 / 0.78 ( 108) link_NAG-ASN : bond 0.00214 / 0.14 ( 48) link_NAG-ASN : angle 1.98918 / 1.34 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 340 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.7940 (ttm) REVERT: A 475 MET cc_start: 0.7308 (mmt) cc_final: 0.7020 (mmt) REVERT: L 79 GLN cc_start: 0.7743 (mp10) cc_final: 0.7330 (mt0) REVERT: L 92 ASN cc_start: 0.8347 (t0) cc_final: 0.7964 (t0) REVERT: H 13 LYS cc_start: 0.7981 (mmtm) cc_final: 0.7457 (mptt) REVERT: H 81 GLU cc_start: 0.5828 (tm-30) cc_final: 0.5585 (tm-30) REVERT: D 104 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7695 (ttm) REVERT: E 92 ASN cc_start: 0.8530 (t0) cc_final: 0.8147 (t0) REVERT: I 10 GLU cc_start: 0.5405 (pt0) cc_final: 0.5172 (pt0) REVERT: I 12 LYS cc_start: 0.8085 (mmtt) cc_final: 0.7876 (mmtp) REVERT: I 13 LYS cc_start: 0.8333 (mmtm) cc_final: 0.8129 (mmtm) REVERT: I 19 LYS cc_start: 0.8175 (mmmt) cc_final: 0.7550 (tttp) REVERT: J 80 ASN cc_start: 0.7552 (p0) cc_final: 0.7319 (p0) REVERT: J 400 ARG cc_start: 0.6627 (ttt180) cc_final: 0.6411 (tpp-160) REVERT: K 78 LEU cc_start: 0.8066 (tp) cc_final: 0.7547 (tt) REVERT: M 544 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8617 (mt) REVERT: M 620 ASN cc_start: 0.7490 (m-40) cc_final: 0.7278 (m-40) REVERT: N 94 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7318 (tt0) REVERT: O 1 GLN cc_start: 0.7269 (mp10) cc_final: 0.6855 (mp10) REVERT: O 10 GLU cc_start: 0.5904 (tt0) cc_final: 0.5407 (pt0) REVERT: O 39 GLN cc_start: 0.7022 (tp40) cc_final: 0.6753 (tm-30) REVERT: O 82 ARG cc_start: 0.6643 (ptp90) cc_final: 0.6195 (ptp90) REVERT: O 100 TYR cc_start: 0.7356 (t80) cc_final: 0.6967 (t80) outliers start: 45 outliers final: 38 residues processed: 365 average time/residue: 0.1785 time to fit residues: 95.6638 Evaluate side-chains 368 residues out of total 2217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 327 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 443 ILE Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 544 LEU Chi-restraints excluded: chain M residue 566 LEU Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain M residue 589 ASP Chi-restraints excluded: chain M residue 612 ASP Chi-restraints excluded: chain M residue 615 SER Chi-restraints excluded: chain N residue 16 CYS Chi-restraints excluded: chain N residue 19 SER Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 35 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN K 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.128235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.101873 restraints weight = 35105.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.103720 restraints weight = 28888.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.104285 restraints weight = 23507.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.104795 restraints weight = 20650.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.105126 restraints weight = 18332.979| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21984 Z= 0.154 Angle : 0.661 8.927 29997 Z= 0.339 Chirality : 0.046 0.268 3597 Planarity : 0.005 0.071 3660 Dihedral : 5.596 58.524 2763 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.12 % Allowed : 16.24 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.17), residues: 2517 helix: 2.01 (0.26), residues: 456 sheet: 0.44 (0.21), residues: 657 loop : -1.03 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 103 TYR 0.022 0.002 TYR I 79 PHE 0.035 0.002 PHE H 29 TRP 0.024 0.001 TRP J 479 HIS 0.007 0.001 HIS O 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (21855) covalent geometry : angle 0.64014 / 0.33 (29649) SS BOND : bond 0.00311 / 0.19 ( 39) SS BOND : angle 1.66478 / 1.25 ( 78) hydrogen bonds : bond 0.04118 / 2.70 ( 855) hydrogen bonds : angle 5.29938 / 3.68 ( 2223) link_ALPHA1-2 : bond 0.00163 / 0.07 ( 3) link_ALPHA1-2 : angle 1.87499 / 1.08 ( 9) link_ALPHA1-3 : bond 0.00633 / 0.28 ( 3) link_ALPHA1-3 : angle 1.19722 / 0.67 ( 9) link_BETA1-4 : bond 0.00310 / 0.19 ( 36) link_BETA1-4 : angle 1.21642 / 0.81 ( 108) link_NAG-ASN : bond 0.00196 / 0.13 ( 48) link_NAG-ASN : angle 1.96167 / 1.33 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3531.03 seconds wall clock time: 62 minutes 24.62 seconds (3744.62 seconds total)