Starting phenix.real_space_refine on Sat Sep 28 20:30:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6myy_9294/09_2024/6myy_9294.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6myy_9294/09_2024/6myy_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6myy_9294/09_2024/6myy_9294.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6myy_9294/09_2024/6myy_9294.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6myy_9294/09_2024/6myy_9294.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6myy_9294/09_2024/6myy_9294.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 12.47, per 1000 atoms: 0.62 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: 7.22 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.82 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: 7.84 Time building geometry restraints manager: 7.83 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: 0.00 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.820 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 48.420 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.810 ------------------------------------------------------------------------------- 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 : 0.015 0.084 20526 Z= 0.951 Angle : 1.366 8.568 27867 Z= 0.801 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (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 TRP 0.017 0.002 TRP D 47 HIS 0.002 0.000 HIS A 374 PHE 0.014 0.002 PHE E 383 TYR 0.016 0.002 TYR B 484 ARG 0.002 0.000 ARG E 298 *********************** 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 fitting. rotamer outliers: 6 poor density : 301 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ASN cc_start: 0.8159 (t0) cc_final: 0.7833 (t0) REVERT: A 464 ASN cc_start: 0.7894 (m-40) cc_final: 0.7377 (t0) REVERT: H 48 MET cc_start: 0.7465 (mmm) cc_final: 0.7076 (mmt) REVERT: B 125 LEU cc_start: 0.9103 (mm) cc_final: 0.8878 (mt) REVERT: B 377 ASN cc_start: 0.8297 (t0) cc_final: 0.7691 (t0) REVERT: B 464 ASN cc_start: 0.7696 (m-40) cc_final: 0.7390 (t0) REVERT: C 32 TYR cc_start: 0.7653 (m-80) cc_final: 0.6765 (m-10) REVERT: D 51 ILE cc_start: 0.9263 (tt) cc_final: 0.9059 (tt) REVERT: D 75 ILE cc_start: 0.8894 (pt) cc_final: 0.8674 (mt) REVERT: D 85 ASP cc_start: 0.8313 (p0) cc_final: 0.8099 (p0) REVERT: E 69 TRP cc_start: 0.8257 (m-90) cc_final: 0.7338 (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: 0.7088 (t0) REVERT: G 75 ILE cc_start: 0.8906 (pt) cc_final: 0.8662 (mt) 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: 0.2941 time to fit residues: 140.3725 Evaluate side-chains 116 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.5980 chunk 172 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20526 Z= 0.233 Angle : 0.712 10.101 27867 Z= 0.336 Chirality : 0.049 0.445 3582 Planarity : 0.004 0.035 3312 Dihedral : 14.369 90.171 5640 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.95 % Favored : 97.92 % Rotamer: Outliers : 1.04 % Allowed : 6.27 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.18), residues: 2256 helix: 1.75 (0.27), residues: 408 sheet: 0.33 (0.19), residues: 738 loop : 0.30 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 571 HIS 0.003 0.001 HIS E 355 PHE 0.016 0.002 PHE B 382 TYR 0.020 0.002 TYR D 90 ARG 0.004 0.000 ARG D 83 *********************** 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 175 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 2.162 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: 0.8178 (t0) cc_final: 0.7942 (t0) REVERT: A 464 ASN cc_start: 0.7833 (m-40) cc_final: 0.7417 (t0) REVERT: A 535 MET cc_start: 0.8792 (mmm) cc_final: 0.8566 (mmm) REVERT: L 29 VAL cc_start: 0.7405 (t) cc_final: 0.6753 (t) REVERT: B 86 LEU cc_start: 0.8616 (mp) cc_final: 0.8367 (mp) REVERT: B 377 ASN cc_start: 0.8200 (t0) cc_final: 0.7918 (t0) REVERT: D 85 ASP cc_start: 0.8577 (p0) cc_final: 0.8304 (p0) REVERT: E 69 TRP cc_start: 0.8258 (m-90) cc_final: 0.7369 (m-10) REVERT: E 377 ASN cc_start: 0.8317 (t0) cc_final: 0.8018 (t0) REVERT: E 464 ASN cc_start: 0.7121 (m-40) cc_final: 0.6821 (t0) REVERT: G 85 ASP cc_start: 0.8771 (p0) cc_final: 0.8411 (p0) outliers start: 21 outliers final: 12 residues processed: 168 average time/residue: 0.2748 time to fit residues: 75.1660 Evaluate side-chains 128 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 2.179 ------------------------------------------------------------------------------- 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 661 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain G residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 224 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 205 optimal weight: 5.9990 chunk 70 optimal weight: 0.1980 chunk 166 optimal weight: 1.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS A 422 GLN B 229 ASN B 355 HIS B 422 GLN E 229 ASN E 355 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 20526 Z= 0.327 Angle : 0.711 8.404 27867 Z= 0.338 Chirality : 0.049 0.573 3582 Planarity : 0.005 0.121 3312 Dihedral : 11.433 78.136 5640 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.81 % Favored : 96.05 % Rotamer: Outliers : 1.69 % Allowed : 6.52 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.18), residues: 2256 helix: 2.74 (0.27), residues: 372 sheet: 0.20 (0.20), residues: 684 loop : -0.01 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 69 HIS 0.006 0.001 HIS A 249 PHE 0.018 0.002 PHE B 383 TYR 0.021 0.002 TYR C 91 ARG 0.006 0.001 ARG F 18 *********************** 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 158 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 124 time to evaluate : 2.057 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: 0.8479 (t0) cc_final: 0.8270 (t0) REVERT: A 464 ASN cc_start: 0.8013 (m-40) cc_final: 0.7524 (t0) REVERT: B 377 ASN cc_start: 0.8323 (t0) cc_final: 0.7946 (t0) REVERT: D 85 ASP cc_start: 0.8758 (p0) cc_final: 0.8467 (p0) REVERT: E 104 MET cc_start: 0.8458 (tpp) cc_final: 0.8252 (ttp) REVERT: E 475 MET cc_start: 0.8213 (mmt) cc_final: 0.7979 (mmt) REVERT: G 85 ASP cc_start: 0.8814 (p0) cc_final: 0.8442 (p0) outliers start: 34 outliers final: 21 residues processed: 146 average time/residue: 0.2570 time to fit residues: 62.6550 Evaluate side-chains 131 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 2.143 ------------------------------------------------------------------------------- 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 641 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain B residue 54 CYS 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 D residue 57 THR 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 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 204 optimal weight: 0.9990 chunk 155 optimal weight: 0.3980 chunk 107 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 208 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20526 Z= 0.193 Angle : 0.608 8.212 27867 Z= 0.283 Chirality : 0.046 0.496 3582 Planarity : 0.004 0.033 3312 Dihedral : 9.337 61.702 5640 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.44 % Favored : 97.43 % Rotamer: Outliers : 1.14 % Allowed : 8.16 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2256 helix: 2.76 (0.28), residues: 384 sheet: 0.26 (0.19), residues: 711 loop : -0.20 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.004 0.001 HIS E 72 PHE 0.016 0.001 PHE E 522 TYR 0.018 0.001 TYR F 91 ARG 0.002 0.000 ARG A 480 *********************** 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 146 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7635 (mmm) cc_final: 0.7363 (mmt) REVERT: B 377 ASN cc_start: 0.8312 (t0) cc_final: 0.8002 (t0) REVERT: D 85 ASP cc_start: 0.8762 (p0) cc_final: 0.8553 (p0) REVERT: E 69 TRP cc_start: 0.8334 (m-90) cc_final: 0.7478 (m-10) REVERT: G 85 ASP cc_start: 0.8771 (p0) cc_final: 0.8502 (p0) outliers start: 23 outliers final: 16 residues processed: 138 average time/residue: 0.2451 time to fit residues: 58.1424 Evaluate side-chains 120 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 2.228 ------------------------------------------------------------------------------- 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 641 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain B residue 295 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 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 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 183 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 3 optimal weight: 0.0070 chunk 164 optimal weight: 0.0670 chunk 90 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 197 optimal weight: 0.5980 chunk 55 optimal weight: 10.0000 overall best weight: 1.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20526 Z= 0.284 Angle : 0.655 7.361 27867 Z= 0.306 Chirality : 0.047 0.456 3582 Planarity : 0.004 0.033 3312 Dihedral : 8.599 57.431 5640 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.81 % Favored : 96.05 % Rotamer: Outliers : 1.84 % Allowed : 8.51 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.18), residues: 2256 helix: 2.74 (0.27), residues: 384 sheet: 0.22 (0.20), residues: 657 loop : -0.37 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 427 HIS 0.004 0.001 HIS E 72 PHE 0.017 0.002 PHE B 383 TYR 0.018 0.002 TYR L 49 ARG 0.003 0.000 ARG G 38 *********************** 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 137 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 100 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 377 ASN cc_start: 0.8313 (t0) cc_final: 0.7999 (t0) REVERT: E 69 TRP cc_start: 0.8392 (m-90) cc_final: 0.7580 (m-10) REVERT: E 475 MET cc_start: 0.8175 (mmt) cc_final: 0.7967 (mmt) REVERT: G 85 ASP cc_start: 0.8836 (p0) cc_final: 0.8600 (p0) outliers start: 37 outliers final: 32 residues processed: 129 average time/residue: 0.2795 time to fit residues: 62.5256 Evaluate side-chains 124 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 92 time to evaluate : 2.245 ------------------------------------------------------------------------------- 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 452 LEU 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 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 295 VAL 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 D residue 23 LYS Chi-restraints excluded: chain D residue 48 MET 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 409 ILE Chi-restraints excluded: chain E residue 452 LEU 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 4 LEU Chi-restraints excluded: chain F residue 75 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 3.9990 chunk 198 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 220 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20526 Z= 0.248 Angle : 0.625 8.246 27867 Z= 0.291 Chirality : 0.046 0.428 3582 Planarity : 0.004 0.032 3312 Dihedral : 8.149 54.711 5640 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.32 % Favored : 96.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.18), residues: 2256 helix: 2.78 (0.27), residues: 384 sheet: 0.11 (0.20), residues: 663 loop : -0.44 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 69 HIS 0.004 0.001 HIS E 72 PHE 0.016 0.001 PHE B 383 TYR 0.013 0.001 TYR L 49 ARG 0.002 0.000 ARG E 480 *********************** 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 134 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 97 time to evaluate : 2.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 THR cc_start: 0.7417 (m) cc_final: 0.7216 (p) REVERT: B 69 TRP cc_start: 0.8143 (m-10) cc_final: 0.7675 (m-10) REVERT: B 209 THR cc_start: 0.7047 (m) cc_final: 0.6743 (p) REVERT: E 69 TRP cc_start: 0.8408 (m-90) cc_final: 0.7474 (m-10) outliers start: 37 outliers final: 28 residues processed: 129 average time/residue: 0.2497 time to fit residues: 55.8529 Evaluate side-chains 116 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 88 time to evaluate : 2.272 ------------------------------------------------------------------------------- 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 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 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 409 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain D residue 48 MET 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 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 57 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 125 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 124 optimal weight: 0.0980 chunk 185 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 219 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 133 optimal weight: 0.0870 chunk 101 optimal weight: 5.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20526 Z= 0.141 Angle : 0.569 8.190 27867 Z= 0.262 Chirality : 0.045 0.392 3582 Planarity : 0.003 0.032 3312 Dihedral : 7.254 53.064 5640 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.59 % Allowed : 9.40 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 2256 helix: 2.87 (0.27), residues: 390 sheet: 0.26 (0.20), residues: 672 loop : -0.34 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 628 HIS 0.004 0.001 HIS H 102 PHE 0.013 0.001 PHE A 383 TYR 0.011 0.001 TYR L 49 ARG 0.002 0.000 ARG A 298 *********************** 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 136 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 104 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7747 (mmt) cc_final: 0.7316 (mmt) REVERT: B 69 TRP cc_start: 0.8181 (m-10) cc_final: 0.7791 (m-10) REVERT: B 377 ASN cc_start: 0.8246 (t0) cc_final: 0.7995 (t0) REVERT: B 530 MET cc_start: 0.7260 (tpp) cc_final: 0.6948 (mmm) REVERT: E 69 TRP cc_start: 0.8376 (m-90) cc_final: 0.7625 (m-10) REVERT: E 377 ASN cc_start: 0.8113 (t0) cc_final: 0.7820 (t0) outliers start: 32 outliers final: 22 residues processed: 133 average time/residue: 0.2599 time to fit residues: 58.2527 Evaluate side-chains 115 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL 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 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 295 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 47 LEU 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 452 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20526 Z= 0.301 Angle : 0.666 9.657 27867 Z= 0.308 Chirality : 0.046 0.403 3582 Planarity : 0.004 0.052 3312 Dihedral : 7.726 56.421 5640 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.12 % Favored : 95.83 % Rotamer: Outliers : 1.59 % Allowed : 9.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.18), residues: 2256 helix: 2.69 (0.27), residues: 390 sheet: 0.11 (0.21), residues: 627 loop : -0.34 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 36 HIS 0.004 0.001 HIS H 35 PHE 0.015 0.001 PHE B 383 TYR 0.017 0.002 TYR B 217 ARG 0.008 0.001 ARG F 54 *********************** 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 122 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 90 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 THR cc_start: 0.7368 (m) cc_final: 0.7137 (p) REVERT: B 69 TRP cc_start: 0.8299 (m-10) cc_final: 0.7436 (m-10) REVERT: B 209 THR cc_start: 0.7117 (m) cc_final: 0.6871 (p) outliers start: 32 outliers final: 28 residues processed: 119 average time/residue: 0.2574 time to fit residues: 52.5467 Evaluate side-chains 113 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 85 time to evaluate : 2.296 ------------------------------------------------------------------------------- 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 452 LEU Chi-restraints excluded: chain A residue 641 ILE 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 295 VAL 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 47 LEU 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 333 ILE 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 30 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 192 optimal weight: 0.6980 chunk 204 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 185 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20526 Z= 0.182 Angle : 0.597 9.968 27867 Z= 0.273 Chirality : 0.045 0.376 3582 Planarity : 0.004 0.044 3312 Dihedral : 7.308 59.405 5640 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.39 % Allowed : 10.00 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 2256 helix: 2.78 (0.27), residues: 390 sheet: 0.28 (0.21), residues: 603 loop : -0.32 (0.18), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 36 HIS 0.003 0.001 HIS B 72 PHE 0.014 0.001 PHE A 383 TYR 0.012 0.001 TYR L 49 ARG 0.005 0.000 ARG F 54 *********************** 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 125 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 97 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 THR cc_start: 0.7275 (m) cc_final: 0.7060 (p) REVERT: A 475 MET cc_start: 0.7811 (mmt) cc_final: 0.7385 (mmt) REVERT: L 87 TYR cc_start: 0.7864 (m-80) cc_final: 0.7639 (m-80) REVERT: B 69 TRP cc_start: 0.8164 (m-10) cc_final: 0.7778 (m-10) REVERT: B 209 THR cc_start: 0.7367 (m) cc_final: 0.7120 (p) REVERT: B 530 MET cc_start: 0.7712 (mmm) cc_final: 0.7375 (tpp) REVERT: E 69 TRP cc_start: 0.8222 (m-90) cc_final: 0.7440 (m-10) outliers start: 28 outliers final: 26 residues processed: 121 average time/residue: 0.2507 time to fit residues: 52.8790 Evaluate side-chains 117 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS 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 295 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 29 VAL 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 30 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 150 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 209 optimal weight: 0.6980 chunk 180 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20526 Z= 0.226 Angle : 0.625 10.147 27867 Z= 0.285 Chirality : 0.045 0.375 3582 Planarity : 0.004 0.044 3312 Dihedral : 7.322 55.949 5640 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.39 % Allowed : 10.05 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2256 helix: 2.73 (0.27), residues: 390 sheet: 0.26 (0.21), residues: 591 loop : -0.36 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP H 36 HIS 0.003 0.001 HIS E 72 PHE 0.014 0.001 PHE B 383 TYR 0.014 0.001 TYR L 49 ARG 0.003 0.000 ARG F 54 ********************** 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 122 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 94 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 THR cc_start: 0.7304 (m) cc_final: 0.7091 (p) REVERT: A 475 MET cc_start: 0.7938 (mmt) cc_final: 0.7533 (mmt) REVERT: L 87 TYR cc_start: 0.7829 (m-80) cc_final: 0.7596 (m-80) REVERT: B 69 TRP cc_start: 0.8200 (m-10) cc_final: 0.7719 (m-10) REVERT: B 209 THR cc_start: 0.7431 (m) cc_final: 0.7181 (p) REVERT: B 530 MET cc_start: 0.7883 (mmm) cc_final: 0.7621 (tpp) REVERT: E 69 TRP cc_start: 0.8271 (m-90) cc_final: 0.7494 (m-10) outliers start: 28 outliers final: 26 residues processed: 117 average time/residue: 0.2481 time to fit residues: 50.6722 Evaluate side-chains 114 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 88 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS 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 295 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 29 VAL 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 333 ILE 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 30 SER 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 192 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 181 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 186 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 33 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN L 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.066731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.055347 restraints weight = 87080.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.056862 restraints weight = 47092.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.057852 restraints weight = 32190.889| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20526 Z= 0.204 Angle : 0.614 10.439 27867 Z= 0.280 Chirality : 0.045 0.365 3582 Planarity : 0.004 0.043 3312 Dihedral : 7.194 59.953 5640 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.44 % Allowed : 10.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.18), residues: 2256 helix: 2.74 (0.27), residues: 390 sheet: 0.09 (0.20), residues: 681 loop : -0.32 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 571 HIS 0.003 0.001 HIS E 72 PHE 0.014 0.001 PHE B 383 TYR 0.013 0.001 TYR L 49 ARG 0.005 0.000 ARG G 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2872.57 seconds wall clock time: 53 minutes 33.22 seconds (3213.22 seconds total)