Starting phenix.real_space_refine on Thu Mar 5 07:24:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6myy_9294/03_2026/6myy_9294.cif Found real_map, /net/cci-nas-00/data/ceres_data/6myy_9294/03_2026/6myy_9294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6myy_9294/03_2026/6myy_9294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6myy_9294/03_2026/6myy_9294.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6myy_9294/03_2026/6myy_9294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6myy_9294/03_2026/6myy_9294.map" } resolution = 3.8 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= 0.000 sd= 0.007 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 129 5.16 5 C 12564 2.51 5 N 3243 2.21 5 O 4203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20139 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4338 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 23, 'TRANS': 526} Chain breaks: 5 Chain: "L" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 767 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4338 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 23, 'TRANS': 526} Chain breaks: 5 Chain: "C" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 767 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain: "D" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4338 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 23, 'TRANS': 526} Chain breaks: 5 Chain: "F" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 767 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain: "G" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "o" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.12, per 1000 atoms: 0.25 Number of scatterers: 20139 At special positions: 0 Unit cell: (149.6, 140.08, 125.12, 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 129 16.00 O 4203 8.00 N 3243 7.00 C 12564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.13 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.05 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS H 60 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 605 " distance=2.20 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.17 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.13 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.02 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.02 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.05 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 459 " - pdb=" SG CYS D 60 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 605 " distance=2.20 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.17 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.13 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.05 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 459 " - pdb=" SG CYS G 60 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS E 605 " distance=2.20 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.17 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN O 4 " - " MAN O 5 " " MAN T 4 " - " MAN T 5 " " MAN c 4 " - " MAN c 5 " " MAN h 4 " - " MAN h 5 " " MAN q 4 " - " MAN q 5 " " MAN v 4 " - " MAN v 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 6 " " MAN M 4 " - " MAN M 5 " " BMA O 3 " - " MAN O 4 " " MAN O 6 " - " MAN O 7 " " BMA R 3 " - " MAN R 4 " " BMA T 3 " - " MAN T 4 " " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 6 " " MAN a 4 " - " MAN a 5 " " BMA c 3 " - " MAN c 4 " " MAN c 6 " - " MAN c 7 " " BMA f 3 " - " MAN f 4 " " BMA h 3 " - " MAN h 4 " " BMA n 3 " - " MAN n 4 " " BMA o 3 " - " MAN o 6 " " MAN o 4 " - " MAN o 5 " " BMA q 3 " - " MAN q 4 " " MAN q 6 " - " MAN q 7 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 6 " " BMA Z 3 " - " MAN Z 5 " " BMA a 3 " - " MAN a 4 " " BMA c 3 " - " MAN c 6 " " BMA n 3 " - " MAN n 5 " " BMA o 3 " - " MAN o 4 " " BMA q 3 " - " MAN q 6 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG A 738 " - " ASN A 357 " " NAG A 744 " - " ASN A 411 " " NAG A 747 " - " ASN A 611 " " NAG A 748 " - " ASN A 637 " " NAG B 738 " - " ASN B 357 " " NAG B 744 " - " ASN B 411 " " NAG B 747 " - " ASN B 611 " " NAG B 748 " - " ASN B 637 " " NAG E 738 " - " ASN E 357 " " NAG E 744 " - " ASN E 411 " " NAG E 747 " - " ASN E 611 " " NAG E 748 " - " ASN E 637 " " NAG I 1 " - " ASN A 88 " " NAG J 1 " - " ASN A 130 " " NAG K 1 " - " ASN A 156 " " NAG M 1 " - " ASN A 197 " " NAG N 1 " - " ASN A 241 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN A 289 " " NAG Q 1 " - " ASN A 301 " " NAG R 1 " - " ASN A 332 " " NAG S 1 " - " ASN A 337 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 442 " " NAG V 1 " - " ASN A 230 " " NAG W 1 " - " ASN A 392 " " NAG X 1 " - " ASN B 88 " " NAG Y 1 " - " ASN B 130 " " NAG Z 1 " - " ASN B 156 " " NAG a 1 " - " ASN B 197 " " NAG b 1 " - " ASN B 241 " " NAG c 1 " - " ASN B 262 " " NAG d 1 " - " ASN B 289 " " NAG e 1 " - " ASN B 301 " " NAG f 1 " - " ASN B 332 " " NAG g 1 " - " ASN B 337 " " NAG h 1 " - " ASN B 386 " " NAG i 1 " - " ASN B 442 " " NAG j 1 " - " ASN B 230 " " NAG k 1 " - " ASN B 392 " " NAG l 1 " - " ASN E 88 " " NAG m 1 " - " ASN E 130 " " NAG n 1 " - " ASN E 156 " " NAG o 1 " - " ASN E 197 " " NAG p 1 " - " ASN E 241 " " NAG q 1 " - " ASN E 262 " " NAG r 1 " - " ASN E 289 " " NAG s 1 " - " ASN E 301 " " NAG t 1 " - " ASN E 332 " " NAG u 1 " - " ASN E 337 " " NAG v 1 " - " ASN E 386 " " NAG w 1 " - " ASN E 442 " " NAG x 1 " - " ASN E 230 " " NAG y 1 " - " ASN E 392 " Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 996.6 milliseconds 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4290 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 45 sheets defined 22.0% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.229A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.769A pdb=" N HIS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'A' and resid 523 through 528 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 542 Processing helix chain 'A' and resid 571 through 596 Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.612A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 662 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.114A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'B' and resid 98 through 116 removed outlier: 4.228A pdb=" N ASP B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 334 through 353 removed outlier: 3.769A pdb=" N HIS B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 475 through 481 Processing helix chain 'B' and resid 482 through 484 No H-bonds generated for 'chain 'B' and resid 482 through 484' Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 571 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.612A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'D' and resid 28 through 32 removed outlier: 4.114A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.229A pdb=" N ASP E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 334 through 353 removed outlier: 3.769A pdb=" N HIS E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 481 Processing helix chain 'E' and resid 482 through 484 No H-bonds generated for 'chain 'E' and resid 482 through 484' Processing helix chain 'E' and resid 523 through 528 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 542 Processing helix chain 'E' and resid 571 through 596 Processing helix chain 'E' and resid 618 through 625 Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.612A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 662 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 28 through 32 removed outlier: 4.114A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.266A pdb=" N VAL A 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL A 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N THR A 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N TYR A 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N CYS A 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 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 94 removed outlier: 3.831A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.240A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.503A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY A 451 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 10.778A pdb=" N LYS A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.955A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N LEU A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.905A pdb=" N VAL A 286 " --> pdb=" O LEU A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 357 through 361 Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 10.905A pdb=" N VAL A 286 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N LEU A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.955A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.778A pdb=" N LYS A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY A 451 " --> pdb=" O LYS A 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 414 through 420 removed outlier: 3.576A pdb=" N PHE A 383 " --> pdb=" O PHE A 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 302 through 312 removed outlier: 6.390A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.777A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.460A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.460A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 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 11 removed outlier: 6.566A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AB7, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.266A pdb=" N VAL B 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL B 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N THR B 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N TYR B 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N CYS B 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.832A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AC3, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.240A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.502A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY B 451 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 10.779A pdb=" N LYS B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N LEU B 453 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 11.955A pdb=" N LEU B 288 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N LEU B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 10.906A pdb=" N VAL B 286 " --> pdb=" O LEU B 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 284 through 298 current: chain 'B' and resid 357 through 361 Processing sheet with id=AC5, first strand: chain 'B' and resid 271 through 273 removed outlier: 10.906A pdb=" N VAL B 286 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N LEU B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.955A pdb=" N LEU B 288 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N LEU B 453 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 10.779A pdb=" N LYS B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY B 451 " --> pdb=" O LYS B 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 443 through 456 current: chain 'B' and resid 414 through 420 removed outlier: 3.576A pdb=" N PHE B 383 " --> pdb=" O PHE B 376 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 302 through 312 removed outlier: 6.390A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.777A pdb=" N SER C 7 " --> pdb=" O SER C 22 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.459A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.459A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.566A pdb=" N MET D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TRP D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AD4, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.266A pdb=" N VAL E 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL E 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N THR E 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N TYR E 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N CYS E 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.832A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD9, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.240A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.502A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY E 451 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 10.779A pdb=" N LYS E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.955A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N LEU E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.905A pdb=" N VAL E 286 " --> pdb=" O LEU E 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 298 current: chain 'E' and resid 357 through 361 Processing sheet with id=AE2, first strand: chain 'E' and resid 271 through 273 removed outlier: 10.905A pdb=" N VAL E 286 " --> pdb=" O LEU E 455 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N LEU E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.955A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.779A pdb=" N LYS E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY E 451 " --> pdb=" O LYS E 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 443 through 456 current: chain 'E' and resid 414 through 420 removed outlier: 3.576A pdb=" N PHE E 383 " --> pdb=" O PHE E 376 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 302 through 312 removed outlier: 6.390A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 5 through 7 removed outlier: 3.777A pdb=" N SER F 7 " --> pdb=" O SER F 22 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.460A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.460A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.565A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 10 through 11 780 hydrogen bonds defined for protein. 1953 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: 3.61 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4680 1.33 - 1.45: 4605 1.45 - 1.57: 11013 1.57 - 1.70: 60 1.70 - 1.82: 168 Bond restraints: 20526 Sorted by residual: bond pdb=" C5 BMA c 3 " pdb=" C6 BMA c 3 " ideal model delta sigma weight residual 1.526 1.610 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C5 BMA O 3 " pdb=" C6 BMA O 3 " ideal model delta sigma weight residual 1.526 1.610 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C5 BMA q 3 " pdb=" C6 BMA q 3 " ideal model delta sigma weight residual 1.526 1.609 -0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C5 BMA M 3 " pdb=" C6 BMA M 3 " ideal model delta sigma weight residual 1.526 1.607 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C5 BMA o 3 " pdb=" C6 BMA o 3 " ideal model delta sigma weight residual 1.526 1.607 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 20521 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 24311 1.71 - 3.43: 2717 3.43 - 5.14: 441 5.14 - 6.85: 302 6.85 - 8.57: 96 Bond angle restraints: 27867 Sorted by residual: angle pdb=" C ALA B 436 " pdb=" N PRO B 437 " pdb=" CA PRO B 437 " ideal model delta sigma weight residual 119.66 126.41 -6.75 7.20e-01 1.93e+00 8.78e+01 angle pdb=" C ALA E 436 " pdb=" N PRO E 437 " pdb=" CA PRO E 437 " ideal model delta sigma weight residual 119.66 126.40 -6.74 7.20e-01 1.93e+00 8.77e+01 angle pdb=" C ALA A 436 " pdb=" N PRO A 437 " pdb=" CA PRO A 437 " ideal model delta sigma weight residual 119.66 126.39 -6.73 7.20e-01 1.93e+00 8.74e+01 angle pdb=" C PHE E 353 " pdb=" N PRO E 354 " pdb=" CA PRO E 354 " ideal model delta sigma weight residual 119.56 128.13 -8.57 1.01e+00 9.80e-01 7.20e+01 angle pdb=" C PHE A 353 " pdb=" N PRO A 354 " pdb=" CA PRO A 354 " ideal model delta sigma weight residual 119.56 128.12 -8.56 1.01e+00 9.80e-01 7.18e+01 ... (remaining 27862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.74: 13389 21.74 - 43.48: 531 43.48 - 65.23: 159 65.23 - 86.97: 144 86.97 - 108.71: 96 Dihedral angle restraints: 14319 sinusoidal: 7656 harmonic: 6663 Sorted by residual: dihedral pdb=" CA PHE E 353 " pdb=" C PHE E 353 " pdb=" N PRO E 354 " pdb=" CA PRO E 354 " ideal model delta harmonic sigma weight residual -180.00 -154.39 -25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA PHE B 353 " pdb=" C PHE B 353 " pdb=" N PRO B 354 " pdb=" CA PRO B 354 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA PHE A 353 " pdb=" C PHE A 353 " pdb=" N PRO A 354 " pdb=" CA PRO A 354 " ideal model delta harmonic sigma weight residual -180.00 -154.48 -25.52 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 14316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 3300 0.130 - 0.261: 238 0.261 - 0.391: 20 0.391 - 0.521: 0 0.521 - 0.651: 24 Chirality restraints: 3582 Sorted by residual: chirality pdb=" C1 BMA c 3 " pdb=" O4 NAG c 2 " pdb=" C2 BMA c 3 " pdb=" O5 BMA c 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.90e+02 chirality pdb=" C1 BMA q 3 " pdb=" O4 NAG q 2 " pdb=" C2 BMA q 3 " pdb=" O5 BMA q 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.89e+02 chirality pdb=" C1 BMA O 3 " pdb=" O4 NAG O 2 " pdb=" C2 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.89e+02 ... (remaining 3579 not shown) Planarity restraints: 3366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 301 " -0.026 2.00e-02 2.50e+03 2.78e-02 9.67e+00 pdb=" CG ASN E 301 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN E 301 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN E 301 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG s 1 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 301 " -0.026 2.00e-02 2.50e+03 2.78e-02 9.66e+00 pdb=" CG ASN A 301 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN A 301 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 301 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 301 " -0.026 2.00e-02 2.50e+03 2.78e-02 9.65e+00 pdb=" CG ASN B 301 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN B 301 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 301 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG e 1 " -0.034 2.00e-02 2.50e+03 ... (remaining 3363 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6348 2.82 - 3.34: 17753 3.34 - 3.86: 33313 3.86 - 4.38: 38387 4.38 - 4.90: 62472 Nonbonded interactions: 158273 Sorted by model distance: nonbonded pdb=" OD1 ASP B 107 " pdb=" NZ LYS B 574 " model vdw 2.302 3.120 nonbonded pdb=" OD1 ASP E 107 " pdb=" NZ LYS E 574 " model vdw 2.303 3.120 nonbonded pdb=" OD1 ASP A 107 " pdb=" NZ LYS A 574 " model vdw 2.303 3.120 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.328 3.040 nonbonded pdb=" OG1 THR E 37 " pdb=" OG1 THR E 499 " model vdw 2.329 3.040 ... (remaining 158268 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'u' selection = chain 'w' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'K' selection = chain 'T' selection = chain 'Z' selection = chain 'h' selection = chain 'n' selection = chain 'v' } ncs_group { reference = (chain 'M' and (resid 1 or resid 4 through 6)) selection = (chain 'O' and (resid 2 or resid 5 through 7)) selection = (chain 'a' and (resid 1 or resid 4 through 6)) selection = (chain 'c' and (resid 2 or resid 5 through 7)) selection = (chain 'o' and (resid 1 or resid 4 through 6)) selection = (chain 'q' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'p' selection = chain 'r' selection = chain 's' } ncs_group { reference = chain 'R' selection = chain 'f' selection = chain 't' } 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: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.220 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 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 : 0.016 0.167 20727 Z= 0.834 Angle : 1.394 13.399 28425 Z= 0.805 Chirality : 0.089 0.651 3582 Planarity : 0.003 0.013 3312 Dihedral : 18.198 108.711 9894 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.32 % Favored : 96.54 % Rotamer: Outliers : 0.30 % Allowed : 1.34 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.23 (0.17), residues: 2256 helix: -0.17 (0.25), residues: 411 sheet: 0.08 (0.19), residues: 717 loop : -0.16 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 298 TYR 0.016 0.002 TYR B 484 PHE 0.014 0.002 PHE E 383 TRP 0.017 0.002 TRP D 47 HIS 0.002 0.000 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.01540 (20526) covalent geometry : angle 1.36600 (27867) SS BOND : bond 0.06274 ( 45) SS BOND : angle 3.92436 ( 90) hydrogen bonds : bond 0.19042 ( 705) hydrogen bonds : angle 8.02491 ( 1953) link_ALPHA1-2 : bond 0.02810 ( 6) link_ALPHA1-2 : angle 1.02245 ( 18) link_ALPHA1-3 : bond 0.03279 ( 21) link_ALPHA1-3 : angle 1.25054 ( 63) link_ALPHA1-6 : bond 0.03163 ( 9) link_ALPHA1-6 : angle 2.35843 ( 27) link_BETA1-4 : bond 0.03171 ( 66) link_BETA1-4 : angle 1.80751 ( 198) link_NAG-ASN : bond 0.02289 ( 54) link_NAG-ASN : angle 2.41139 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 301 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ASN cc_start: 0.8159 (t0) cc_final: 0.7832 (t0) REVERT: A 464 ASN cc_start: 0.7894 (m-40) cc_final: 0.7379 (t0) REVERT: H 48 MET cc_start: 0.7465 (mmm) cc_final: 0.7075 (mmt) REVERT: B 125 LEU cc_start: 0.9103 (mm) cc_final: 0.8880 (mt) REVERT: B 377 ASN cc_start: 0.8297 (t0) cc_final: 0.7694 (t0) REVERT: B 464 ASN cc_start: 0.7696 (m-40) cc_final: 0.7388 (t0) REVERT: C 32 TYR cc_start: 0.7653 (m-80) cc_final: 0.6764 (m-10) REVERT: D 51 ILE cc_start: 0.9263 (tt) cc_final: 0.9060 (tt) REVERT: D 85 ASP cc_start: 0.8313 (p0) cc_final: 0.8072 (p0) REVERT: E 69 TRP cc_start: 0.8257 (m-90) cc_final: 0.7334 (m-10) REVERT: E 377 ASN cc_start: 0.8376 (t0) cc_final: 0.7932 (t0) REVERT: E 464 ASN cc_start: 0.7592 (m-40) cc_final: 0.7087 (t0) REVERT: G 85 ASP cc_start: 0.8538 (p0) cc_final: 0.8266 (p0) outliers start: 6 outliers final: 0 residues processed: 307 average time/residue: 0.1327 time to fit residues: 63.8832 Evaluate side-chains 112 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS L 37 GLN B 216 HIS B 543 ASN C 37 GLN E 216 HIS E 374 HIS F 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.070241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.058686 restraints weight = 86700.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.060334 restraints weight = 46192.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.061422 restraints weight = 31085.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.062142 restraints weight = 24248.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.062507 restraints weight = 20634.129| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20727 Z= 0.151 Angle : 0.759 13.587 28425 Z= 0.345 Chirality : 0.048 0.357 3582 Planarity : 0.004 0.034 3312 Dihedral : 14.170 89.441 5640 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.82 % Favored : 98.05 % Rotamer: Outliers : 1.09 % Allowed : 6.37 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.81 (0.18), residues: 2256 helix: 1.75 (0.27), residues: 408 sheet: 0.38 (0.19), residues: 735 loop : 0.33 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 83 TYR 0.020 0.002 TYR D 90 PHE 0.017 0.002 PHE B 382 TRP 0.013 0.001 TRP E 571 HIS 0.003 0.001 HIS E 355 Details of bonding type rmsd covalent geometry : bond 0.00331 (20526) covalent geometry : angle 0.71373 (27867) SS BOND : bond 0.00210 ( 45) SS BOND : angle 0.93033 ( 90) hydrogen bonds : bond 0.05338 ( 705) hydrogen bonds : angle 6.02645 ( 1953) link_ALPHA1-2 : bond 0.00735 ( 6) link_ALPHA1-2 : angle 1.62519 ( 18) link_ALPHA1-3 : bond 0.00881 ( 21) link_ALPHA1-3 : angle 2.16089 ( 63) link_ALPHA1-6 : bond 0.00897 ( 9) link_ALPHA1-6 : angle 1.91533 ( 27) link_BETA1-4 : bond 0.00577 ( 66) link_BETA1-4 : angle 2.23443 ( 198) link_NAG-ASN : bond 0.00448 ( 54) link_NAG-ASN : angle 2.03545 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ASN cc_start: 0.8351 (t0) cc_final: 0.8063 (t0) REVERT: A 426 MET cc_start: 0.8320 (mmm) cc_final: 0.7680 (tpp) REVERT: A 464 ASN cc_start: 0.7864 (m-40) cc_final: 0.7345 (t0) REVERT: L 29 VAL cc_start: 0.7711 (t) cc_final: 0.7045 (t) REVERT: B 69 TRP cc_start: 0.8457 (m-10) cc_final: 0.7505 (m-10) REVERT: B 86 LEU cc_start: 0.8991 (mp) cc_final: 0.8754 (mp) REVERT: B 377 ASN cc_start: 0.8333 (t0) cc_final: 0.8012 (t0) REVERT: B 464 ASN cc_start: 0.7254 (m-40) cc_final: 0.7023 (t0) REVERT: E 69 TRP cc_start: 0.8440 (m-90) cc_final: 0.7288 (m-10) REVERT: E 100 MET cc_start: 0.8611 (mtp) cc_final: 0.8394 (mtp) REVERT: E 377 ASN cc_start: 0.8325 (t0) cc_final: 0.8067 (t0) REVERT: E 464 ASN cc_start: 0.7224 (m-40) cc_final: 0.6797 (t0) REVERT: F 87 TYR cc_start: 0.8070 (m-80) cc_final: 0.7842 (m-80) REVERT: G 69 MET cc_start: 0.8404 (mtm) cc_final: 0.8187 (mtt) REVERT: G 80 MET cc_start: 0.8778 (tmm) cc_final: 0.8577 (tmm) REVERT: G 85 ASP cc_start: 0.9064 (p0) cc_final: 0.8853 (p0) outliers start: 22 outliers final: 14 residues processed: 169 average time/residue: 0.1275 time to fit residues: 35.1434 Evaluate side-chains 129 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 42 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 355 HIS A 422 GLN B 229 ASN B 355 HIS B 422 GLN E 229 ASN E 355 HIS E 422 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.066558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.054973 restraints weight = 88842.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.056503 restraints weight = 48563.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.057504 restraints weight = 33427.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.058181 restraints weight = 26519.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.058570 restraints weight = 22810.009| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 20727 Z= 0.258 Angle : 0.797 10.541 28425 Z= 0.371 Chirality : 0.050 0.378 3582 Planarity : 0.005 0.066 3312 Dihedral : 11.522 77.060 5640 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.95 % Favored : 95.92 % Rotamer: Outliers : 1.94 % Allowed : 6.87 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.60 (0.18), residues: 2256 helix: 2.52 (0.27), residues: 375 sheet: 0.24 (0.20), residues: 678 loop : -0.13 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 18 TYR 0.017 0.002 TYR L 91 PHE 0.020 0.002 PHE B 383 TRP 0.042 0.002 TRP A 69 HIS 0.007 0.002 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00573 (20526) covalent geometry : angle 0.75826 (27867) SS BOND : bond 0.00327 ( 45) SS BOND : angle 1.02816 ( 90) hydrogen bonds : bond 0.04913 ( 705) hydrogen bonds : angle 5.72630 ( 1953) link_ALPHA1-2 : bond 0.00779 ( 6) link_ALPHA1-2 : angle 1.72651 ( 18) link_ALPHA1-3 : bond 0.00992 ( 21) link_ALPHA1-3 : angle 1.58144 ( 63) link_ALPHA1-6 : bond 0.01072 ( 9) link_ALPHA1-6 : angle 2.53898 ( 27) link_BETA1-4 : bond 0.00524 ( 66) link_BETA1-4 : angle 2.11228 ( 198) link_NAG-ASN : bond 0.00549 ( 54) link_NAG-ASN : angle 2.04416 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ASN cc_start: 0.8585 (t0) cc_final: 0.8379 (t0) REVERT: L 29 VAL cc_start: 0.7800 (OUTLIER) cc_final: 0.6477 (t) REVERT: B 377 ASN cc_start: 0.8432 (t0) cc_final: 0.8060 (t0) REVERT: E 69 TRP cc_start: 0.8613 (m-90) cc_final: 0.7422 (m-10) REVERT: E 100 MET cc_start: 0.8638 (mtp) cc_final: 0.8292 (mtp) REVERT: E 104 MET cc_start: 0.9149 (tpp) cc_final: 0.8842 (ttp) REVERT: E 475 MET cc_start: 0.7916 (mmt) cc_final: 0.7687 (mmt) REVERT: G 85 ASP cc_start: 0.9010 (p0) cc_final: 0.8760 (p0) outliers start: 39 outliers final: 27 residues processed: 143 average time/residue: 0.1238 time to fit residues: 29.6481 Evaluate side-chains 132 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 182 optimal weight: 0.9990 chunk 217 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 167 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 216 optimal weight: 4.9990 chunk 213 optimal weight: 9.9990 chunk 126 optimal weight: 0.0040 chunk 222 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.068025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.056490 restraints weight = 87762.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.058062 restraints weight = 47350.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.059126 restraints weight = 32323.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.059796 restraints weight = 25412.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.060223 restraints weight = 21861.717| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20727 Z= 0.125 Angle : 0.647 8.269 28425 Z= 0.292 Chirality : 0.046 0.280 3582 Planarity : 0.004 0.034 3312 Dihedral : 9.379 61.620 5640 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.53 % Favored : 97.38 % Rotamer: Outliers : 1.14 % Allowed : 8.56 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.77 (0.18), residues: 2256 helix: 2.96 (0.27), residues: 375 sheet: 0.32 (0.20), residues: 681 loop : -0.11 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 18 TYR 0.018 0.001 TYR C 91 PHE 0.015 0.001 PHE B 383 TRP 0.017 0.001 TRP B 571 HIS 0.003 0.001 HIS H 102 Details of bonding type rmsd covalent geometry : bond 0.00260 (20526) covalent geometry : angle 0.60723 (27867) SS BOND : bond 0.00327 ( 45) SS BOND : angle 0.77160 ( 90) hydrogen bonds : bond 0.04043 ( 705) hydrogen bonds : angle 5.31668 ( 1953) link_ALPHA1-2 : bond 0.00778 ( 6) link_ALPHA1-2 : angle 1.97759 ( 18) link_ALPHA1-3 : bond 0.01122 ( 21) link_ALPHA1-3 : angle 1.52337 ( 63) link_ALPHA1-6 : bond 0.01360 ( 9) link_ALPHA1-6 : angle 3.39700 ( 27) link_BETA1-4 : bond 0.00499 ( 66) link_BETA1-4 : angle 1.90760 ( 198) link_NAG-ASN : bond 0.00341 ( 54) link_NAG-ASN : angle 1.43316 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ASN cc_start: 0.8460 (t0) cc_final: 0.8256 (t0) REVERT: A 475 MET cc_start: 0.7709 (mmm) cc_final: 0.7230 (mmt) REVERT: H 17 SER cc_start: 0.8611 (p) cc_final: 0.8151 (m) REVERT: B 377 ASN cc_start: 0.8389 (t0) cc_final: 0.8071 (t0) REVERT: E 69 TRP cc_start: 0.8486 (m-90) cc_final: 0.7403 (m-10) REVERT: E 100 MET cc_start: 0.8636 (mtp) cc_final: 0.8228 (mtp) outliers start: 23 outliers final: 15 residues processed: 141 average time/residue: 0.1172 time to fit residues: 28.3907 Evaluate side-chains 114 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 185 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 22 optimal weight: 0.0470 chunk 112 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 60 optimal weight: 0.0070 chunk 100 optimal weight: 0.4980 chunk 204 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 109 optimal weight: 0.3980 chunk 101 optimal weight: 0.7980 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.068990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.057566 restraints weight = 86942.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.059210 restraints weight = 45859.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.060300 restraints weight = 30655.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.061016 restraints weight = 23831.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.061435 restraints weight = 20244.209| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20727 Z= 0.104 Angle : 0.613 8.316 28425 Z= 0.275 Chirality : 0.045 0.253 3582 Planarity : 0.004 0.040 3312 Dihedral : 7.661 56.968 5640 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.54 % Allowed : 8.61 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.18), residues: 2256 helix: 2.89 (0.27), residues: 390 sheet: 0.30 (0.19), residues: 723 loop : -0.17 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 18 TYR 0.018 0.001 TYR D 90 PHE 0.012 0.001 PHE B 53 TRP 0.025 0.001 TRP B 571 HIS 0.004 0.001 HIS H 102 Details of bonding type rmsd covalent geometry : bond 0.00210 (20526) covalent geometry : angle 0.57489 (27867) SS BOND : bond 0.00209 ( 45) SS BOND : angle 0.65199 ( 90) hydrogen bonds : bond 0.03600 ( 705) hydrogen bonds : angle 4.98481 ( 1953) link_ALPHA1-2 : bond 0.00758 ( 6) link_ALPHA1-2 : angle 2.10025 ( 18) link_ALPHA1-3 : bond 0.01164 ( 21) link_ALPHA1-3 : angle 1.36802 ( 63) link_ALPHA1-6 : bond 0.01324 ( 9) link_ALPHA1-6 : angle 3.16915 ( 27) link_BETA1-4 : bond 0.00516 ( 66) link_BETA1-4 : angle 1.76204 ( 198) link_NAG-ASN : bond 0.00341 ( 54) link_NAG-ASN : angle 1.44503 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ASN cc_start: 0.8382 (t0) cc_final: 0.8179 (t0) REVERT: A 475 MET cc_start: 0.7515 (mmm) cc_final: 0.7139 (mmt) REVERT: B 69 TRP cc_start: 0.8433 (m-10) cc_final: 0.7566 (m-10) REVERT: B 377 ASN cc_start: 0.8347 (t0) cc_final: 0.8082 (t0) REVERT: D 69 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7920 (mtm) REVERT: E 69 TRP cc_start: 0.8466 (m-90) cc_final: 0.7825 (m-10) REVERT: E 100 MET cc_start: 0.8633 (mtp) cc_final: 0.8205 (mtp) REVERT: G 51 ILE cc_start: 0.9515 (tt) cc_final: 0.9190 (tp) outliers start: 31 outliers final: 22 residues processed: 146 average time/residue: 0.1243 time to fit residues: 30.3758 Evaluate side-chains 120 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 218 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.067592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.056179 restraints weight = 87476.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.057783 restraints weight = 46453.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.058839 restraints weight = 31244.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.059536 restraints weight = 24341.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.059965 restraints weight = 20759.010| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20727 Z= 0.148 Angle : 0.633 10.549 28425 Z= 0.285 Chirality : 0.045 0.258 3582 Planarity : 0.004 0.057 3312 Dihedral : 7.380 54.698 5640 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.79 % Allowed : 9.50 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.72 (0.18), residues: 2256 helix: 2.87 (0.27), residues: 390 sheet: 0.33 (0.20), residues: 657 loop : -0.19 (0.19), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 54 TYR 0.014 0.001 TYR E 638 PHE 0.014 0.001 PHE B 383 TRP 0.010 0.001 TRP E 628 HIS 0.003 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00324 (20526) covalent geometry : angle 0.59553 (27867) SS BOND : bond 0.00215 ( 45) SS BOND : angle 0.67122 ( 90) hydrogen bonds : bond 0.03703 ( 705) hydrogen bonds : angle 4.97531 ( 1953) link_ALPHA1-2 : bond 0.00774 ( 6) link_ALPHA1-2 : angle 1.84811 ( 18) link_ALPHA1-3 : bond 0.01034 ( 21) link_ALPHA1-3 : angle 1.41455 ( 63) link_ALPHA1-6 : bond 0.01175 ( 9) link_ALPHA1-6 : angle 3.09538 ( 27) link_BETA1-4 : bond 0.00478 ( 66) link_BETA1-4 : angle 1.82589 ( 198) link_NAG-ASN : bond 0.00341 ( 54) link_NAG-ASN : angle 1.49933 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 0.650 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 475 MET cc_start: 0.7601 (mmm) cc_final: 0.7266 (mmt) REVERT: B 377 ASN cc_start: 0.8346 (t0) cc_final: 0.8078 (t0) REVERT: B 530 MET cc_start: 0.8322 (mmm) cc_final: 0.8116 (mmm) REVERT: E 69 TRP cc_start: 0.8450 (m-90) cc_final: 0.7498 (m-10) REVERT: E 100 MET cc_start: 0.8559 (mtp) cc_final: 0.8334 (mtp) REVERT: G 96 LYS cc_start: 0.8353 (pptt) cc_final: 0.7483 (ptmm) outliers start: 36 outliers final: 28 residues processed: 126 average time/residue: 0.1103 time to fit residues: 24.3215 Evaluate side-chains 124 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 30 optimal weight: 1.9990 chunk 213 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 164 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.067803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.056290 restraints weight = 88012.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.057853 restraints weight = 48149.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.058881 restraints weight = 32976.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.059556 restraints weight = 26053.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.060011 restraints weight = 22422.302| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20727 Z= 0.134 Angle : 0.617 10.131 28425 Z= 0.277 Chirality : 0.044 0.239 3582 Planarity : 0.003 0.033 3312 Dihedral : 7.074 54.112 5640 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.74 % Allowed : 9.05 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.68 (0.18), residues: 2256 helix: 2.80 (0.27), residues: 390 sheet: 0.27 (0.20), residues: 699 loop : -0.19 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 54 TYR 0.017 0.001 TYR E 638 PHE 0.015 0.001 PHE A 383 TRP 0.020 0.001 TRP B 69 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00291 (20526) covalent geometry : angle 0.58032 (27867) SS BOND : bond 0.00203 ( 45) SS BOND : angle 0.64736 ( 90) hydrogen bonds : bond 0.03607 ( 705) hydrogen bonds : angle 4.92788 ( 1953) link_ALPHA1-2 : bond 0.00773 ( 6) link_ALPHA1-2 : angle 1.89413 ( 18) link_ALPHA1-3 : bond 0.01045 ( 21) link_ALPHA1-3 : angle 1.38289 ( 63) link_ALPHA1-6 : bond 0.01179 ( 9) link_ALPHA1-6 : angle 3.03351 ( 27) link_BETA1-4 : bond 0.00483 ( 66) link_BETA1-4 : angle 1.78675 ( 198) link_NAG-ASN : bond 0.00339 ( 54) link_NAG-ASN : angle 1.46436 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.646 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: B 377 ASN cc_start: 0.8365 (t0) cc_final: 0.8106 (t0) REVERT: E 69 TRP cc_start: 0.8571 (m-90) cc_final: 0.7596 (m-10) REVERT: E 100 MET cc_start: 0.8619 (mtp) cc_final: 0.8328 (mtp) REVERT: G 69 MET cc_start: 0.8248 (mtp) cc_final: 0.8031 (mtt) outliers start: 35 outliers final: 31 residues processed: 126 average time/residue: 0.1121 time to fit residues: 24.6819 Evaluate side-chains 124 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 121 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 223 optimal weight: 0.2980 chunk 95 optimal weight: 0.7980 chunk 178 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.067393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.055942 restraints weight = 88125.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.057483 restraints weight = 48192.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.058498 restraints weight = 33061.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.059173 restraints weight = 26130.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.059608 restraints weight = 22488.885| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20727 Z= 0.145 Angle : 0.633 10.231 28425 Z= 0.284 Chirality : 0.044 0.236 3582 Planarity : 0.003 0.032 3312 Dihedral : 6.981 54.661 5640 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.84 % Allowed : 9.35 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.66 (0.18), residues: 2256 helix: 2.60 (0.27), residues: 408 sheet: 0.27 (0.20), residues: 654 loop : -0.17 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 38 TYR 0.016 0.001 TYR L 49 PHE 0.014 0.001 PHE B 383 TRP 0.041 0.001 TRP B 69 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00319 (20526) covalent geometry : angle 0.59568 (27867) SS BOND : bond 0.00197 ( 45) SS BOND : angle 0.65516 ( 90) hydrogen bonds : bond 0.03656 ( 705) hydrogen bonds : angle 4.91164 ( 1953) link_ALPHA1-2 : bond 0.00781 ( 6) link_ALPHA1-2 : angle 1.82552 ( 18) link_ALPHA1-3 : bond 0.00994 ( 21) link_ALPHA1-3 : angle 1.38067 ( 63) link_ALPHA1-6 : bond 0.01161 ( 9) link_ALPHA1-6 : angle 2.99072 ( 27) link_BETA1-4 : bond 0.00482 ( 66) link_BETA1-4 : angle 1.81619 ( 198) link_NAG-ASN : bond 0.00350 ( 54) link_NAG-ASN : angle 1.56542 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 0.812 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: B 530 MET cc_start: 0.6812 (tpp) cc_final: 0.6512 (mmm) REVERT: E 100 MET cc_start: 0.8675 (mtp) cc_final: 0.8374 (mtp) outliers start: 37 outliers final: 34 residues processed: 121 average time/residue: 0.1084 time to fit residues: 23.0048 Evaluate side-chains 123 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 42 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.066316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.055104 restraints weight = 87683.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.056534 restraints weight = 49691.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.057462 restraints weight = 34851.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.058087 restraints weight = 27928.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.058490 restraints weight = 24241.084| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20727 Z= 0.193 Angle : 0.687 9.567 28425 Z= 0.311 Chirality : 0.045 0.236 3582 Planarity : 0.004 0.033 3312 Dihedral : 7.418 56.296 5640 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 1.89 % Allowed : 9.45 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.51 (0.18), residues: 2256 helix: 2.78 (0.27), residues: 384 sheet: 0.14 (0.21), residues: 627 loop : -0.30 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 18 TYR 0.018 0.002 TYR L 49 PHE 0.016 0.001 PHE B 383 TRP 0.070 0.002 TRP B 69 HIS 0.004 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00429 (20526) covalent geometry : angle 0.65028 (27867) SS BOND : bond 0.00226 ( 45) SS BOND : angle 0.75468 ( 90) hydrogen bonds : bond 0.03935 ( 705) hydrogen bonds : angle 5.08073 ( 1953) link_ALPHA1-2 : bond 0.00788 ( 6) link_ALPHA1-2 : angle 1.76802 ( 18) link_ALPHA1-3 : bond 0.00969 ( 21) link_ALPHA1-3 : angle 1.45548 ( 63) link_ALPHA1-6 : bond 0.01181 ( 9) link_ALPHA1-6 : angle 3.06499 ( 27) link_BETA1-4 : bond 0.00474 ( 66) link_BETA1-4 : angle 1.86537 ( 198) link_NAG-ASN : bond 0.00389 ( 54) link_NAG-ASN : angle 1.66975 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 86 time to evaluate : 0.919 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 209 THR cc_start: 0.7296 (m) cc_final: 0.6981 (p) REVERT: L 87 TYR cc_start: 0.8184 (m-80) cc_final: 0.7821 (m-80) REVERT: B 209 THR cc_start: 0.7020 (m) cc_final: 0.6790 (p) REVERT: B 530 MET cc_start: 0.7359 (tpp) cc_final: 0.6981 (mpp) REVERT: E 69 TRP cc_start: 0.8397 (m-90) cc_final: 0.7476 (m-90) REVERT: E 100 MET cc_start: 0.8639 (mtp) cc_final: 0.8374 (mtp) REVERT: E 626 MET cc_start: 0.7077 (ttm) cc_final: 0.6744 (ttm) outliers start: 38 outliers final: 32 residues processed: 117 average time/residue: 0.1093 time to fit residues: 22.1428 Evaluate side-chains 115 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 102 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 213 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 83 optimal weight: 0.1980 chunk 114 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 222 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.067231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.055851 restraints weight = 88002.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.057363 restraints weight = 47686.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.058392 restraints weight = 32665.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.058999 restraints weight = 25691.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.059111 restraints weight = 22189.739| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20727 Z= 0.127 Angle : 0.630 10.126 28425 Z= 0.282 Chirality : 0.044 0.221 3582 Planarity : 0.003 0.033 3312 Dihedral : 6.961 54.332 5640 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.54 % Allowed : 10.10 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.55 (0.18), residues: 2256 helix: 2.56 (0.27), residues: 408 sheet: 0.19 (0.20), residues: 639 loop : -0.26 (0.19), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 18 TYR 0.014 0.001 TYR L 49 PHE 0.014 0.001 PHE A 383 TRP 0.041 0.001 TRP B 69 HIS 0.002 0.001 HIS H 102 Details of bonding type rmsd covalent geometry : bond 0.00275 (20526) covalent geometry : angle 0.59347 (27867) SS BOND : bond 0.00195 ( 45) SS BOND : angle 0.67377 ( 90) hydrogen bonds : bond 0.03638 ( 705) hydrogen bonds : angle 4.93569 ( 1953) link_ALPHA1-2 : bond 0.00869 ( 6) link_ALPHA1-2 : angle 1.93687 ( 18) link_ALPHA1-3 : bond 0.01008 ( 21) link_ALPHA1-3 : angle 1.38468 ( 63) link_ALPHA1-6 : bond 0.01198 ( 9) link_ALPHA1-6 : angle 2.93828 ( 27) link_BETA1-4 : bond 0.00502 ( 66) link_BETA1-4 : angle 1.79256 ( 198) link_NAG-ASN : bond 0.00271 ( 54) link_NAG-ASN : angle 1.48717 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.503 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 209 THR cc_start: 0.7292 (m) cc_final: 0.6978 (p) REVERT: L 87 TYR cc_start: 0.8155 (m-80) cc_final: 0.7806 (m-80) REVERT: H 69 MET cc_start: 0.8425 (mmt) cc_final: 0.7889 (mmt) REVERT: B 209 THR cc_start: 0.7265 (m) cc_final: 0.7016 (p) REVERT: B 530 MET cc_start: 0.7310 (tpp) cc_final: 0.7067 (mpp) REVERT: E 69 TRP cc_start: 0.8390 (m-90) cc_final: 0.7337 (m-10) REVERT: E 100 MET cc_start: 0.8658 (mtp) cc_final: 0.8364 (mtp) REVERT: E 415 MET cc_start: 0.7575 (ppp) cc_final: 0.7247 (ppp) REVERT: G 69 MET cc_start: 0.8225 (mtp) cc_final: 0.7829 (mtt) outliers start: 31 outliers final: 30 residues processed: 119 average time/residue: 0.1093 time to fit residues: 22.2270 Evaluate side-chains 120 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 174 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 16 optimal weight: 0.0570 chunk 205 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 160 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 208 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.067681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.056388 restraints weight = 87237.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.057918 restraints weight = 47067.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.058943 restraints weight = 32025.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.059568 restraints weight = 25143.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.060009 restraints weight = 21696.269| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20727 Z= 0.108 Angle : 0.609 10.554 28425 Z= 0.271 Chirality : 0.044 0.216 3582 Planarity : 0.003 0.033 3312 Dihedral : 6.546 54.062 5640 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.54 % Allowed : 9.95 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.61 (0.18), residues: 2256 helix: 2.63 (0.27), residues: 408 sheet: 0.29 (0.20), residues: 636 loop : -0.26 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 18 TYR 0.015 0.001 TYR L 49 PHE 0.013 0.001 PHE A 383 TRP 0.033 0.001 TRP B 69 HIS 0.003 0.001 HIS H 102 Details of bonding type rmsd covalent geometry : bond 0.00228 (20526) covalent geometry : angle 0.57238 (27867) SS BOND : bond 0.00179 ( 45) SS BOND : angle 0.64505 ( 90) hydrogen bonds : bond 0.03410 ( 705) hydrogen bonds : angle 4.80570 ( 1953) link_ALPHA1-2 : bond 0.00854 ( 6) link_ALPHA1-2 : angle 1.97751 ( 18) link_ALPHA1-3 : bond 0.00996 ( 21) link_ALPHA1-3 : angle 1.34872 ( 63) link_ALPHA1-6 : bond 0.01188 ( 9) link_ALPHA1-6 : angle 2.78990 ( 27) link_BETA1-4 : bond 0.00511 ( 66) link_BETA1-4 : angle 1.77420 ( 198) link_NAG-ASN : bond 0.00271 ( 54) link_NAG-ASN : angle 1.51499 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2407.33 seconds wall clock time: 42 minutes 58.25 seconds (2578.25 seconds total)