Starting phenix.real_space_refine on Sat Sep 28 19:02:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vn0_21246/09_2024/6vn0_21246.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vn0_21246/09_2024/6vn0_21246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vn0_21246/09_2024/6vn0_21246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vn0_21246/09_2024/6vn0_21246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vn0_21246/09_2024/6vn0_21246.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vn0_21246/09_2024/6vn0_21246.cif" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.051 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 126 5.16 5 C 12525 2.51 5 N 3306 2.21 5 O 4005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 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: 19962 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3378 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 4 Chain: "B" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "H" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3378 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 4 Chain: "E" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "G" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "J" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3378 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 4 Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "I" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "K" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "M" 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: "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: 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: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 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: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 11.70, per 1000 atoms: 0.59 Number of scatterers: 19962 At special positions: 0 Unit cell: (141.11, 145.23, 119.48, 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 126 16.00 O 4005 8.00 N 3306 7.00 C 12525 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.09 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.18 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.05 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.08 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.10 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.09 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.18 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.05 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.08 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.10 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.02 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.09 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.05 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.18 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.05 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.08 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.10 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " 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 Q 4 " - " MAN Q 5 " " MAN b 4 " - " MAN b 5 " " MAN m 4 " - " MAN m 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA Q 3 " - " MAN Q 4 " " BMA X 3 " - " MAN X 4 " " BMA b 3 " - " MAN b 4 " " BMA i 3 " - " MAN i 4 " " BMA m 3 " - " MAN m 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA X 3 " - " MAN X 5 " " BMA i 3 " - " MAN i 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " NAG-ASN " NAG A 619 " - " ASN A 295 " " NAG A 622 " - " ASN A 355 " " NAG A 629 " - " ASN A 133 " " NAG A 632 " - " ASN A 301 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 611 " " NAG C 619 " - " ASN C 295 " " NAG C 622 " - " ASN C 355 " " NAG C 629 " - " ASN C 133 " " NAG C 632 " - " ASN C 301 " " NAG D 619 " - " ASN D 295 " " NAG D 622 " - " ASN D 355 " " NAG D 629 " - " ASN D 133 " " NAG D 632 " - " ASN D 301 " " NAG E 701 " - " ASN E 618 " " NAG E 702 " - " ASN E 637 " " NAG E 703 " - " ASN E 611 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 611 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 156 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN A 234 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 276 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 392 " " NAG V 1 " - " ASN A 197 " " NAG W 1 " - " ASN A 448 " " NAG X 1 " - " ASN C 88 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 160 " " NAG a 1 " - " ASN C 234 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 276 " " NAG d 1 " - " ASN C 332 " " NAG e 1 " - " ASN C 386 " " NAG f 1 " - " ASN C 392 " " NAG g 1 " - " ASN C 197 " " NAG h 1 " - " ASN C 448 " " NAG i 1 " - " ASN D 88 " " NAG j 1 " - " ASN D 156 " " NAG k 1 " - " ASN D 160 " " NAG l 1 " - " ASN D 234 " " NAG m 1 " - " ASN D 262 " " NAG n 1 " - " ASN D 276 " " NAG o 1 " - " ASN D 332 " " NAG p 1 " - " ASN D 386 " " NAG q 1 " - " ASN D 392 " " NAG r 1 " - " ASN D 197 " " NAG s 1 " - " ASN D 448 " Time building additional restraints: 5.63 Conformation dependent library (CDL) restraints added in 2.2 seconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4362 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 23.1% alpha, 37.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.043A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 476 through 484 removed outlier: 5.134A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 528 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 572 through 597 removed outlier: 3.525A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 646 Processing helix chain 'B' and resid 648 through 661 Processing helix chain 'H' and resid 28 through 32 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 'L' and resid 79 through 83 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 334 through 354 removed outlier: 4.043A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 476 through 484 removed outlier: 5.133A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 528 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 537 through 542 Processing helix chain 'E' and resid 547 through 551 Processing helix chain 'E' and resid 572 through 597 removed outlier: 3.525A pdb=" N LEU E 576 " --> pdb=" O GLY E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 626 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 646 Processing helix chain 'E' and resid 648 through 661 Processing helix chain 'G' and resid 28 through 32 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 helix chain 'J' and resid 79 through 83 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 99 through 117 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 334 through 354 removed outlier: 4.043A pdb=" N LYS D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 476 through 484 removed outlier: 5.133A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 528 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 542 Processing helix chain 'F' and resid 547 through 551 Processing helix chain 'F' and resid 572 through 597 removed outlier: 3.525A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 626 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 646 Processing helix chain 'F' and resid 648 through 661 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.158A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N CYS B 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 removed outlier: 5.513A pdb=" N ILE A 215 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY A 250 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR A 217 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.875A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.586A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.814A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.486A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.630A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.158A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 55 removed outlier: 5.514A pdb=" N ILE C 215 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY C 250 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR C 217 " --> pdb=" O THR C 248 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.875A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AC3, first strand: chain 'C' and resid 181 through 182 Processing sheet with id=AC4, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.586A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.814A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.486A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.630A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 13 Processing sheet with id=AD4, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.158A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'D' and resid 53 through 55 removed outlier: 5.513A pdb=" N ILE D 215 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY D 250 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR D 217 " --> pdb=" O THR D 248 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 91 through 94 removed outlier: 3.875A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 130 through 133 Processing sheet with id=AD9, first strand: chain 'D' and resid 181 through 182 Processing sheet with id=AE1, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.585A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 11.337A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.814A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.337A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 304 through 312 removed outlier: 6.486A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.630A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 13 795 hydrogen bonds defined for protein. 1980 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: 7.36 Time building geometry restraints manager: 6.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 5262 1.33 - 1.47: 6322 1.47 - 1.60: 8620 1.60 - 1.74: 13 1.74 - 1.88: 159 Bond restraints: 20376 Sorted by residual: bond pdb=" CB HIS I 32 " pdb=" CG HIS I 32 " ideal model delta sigma weight residual 1.497 1.435 0.062 1.40e-02 5.10e+03 1.94e+01 bond pdb=" CB HIS G 32 " pdb=" CG HIS G 32 " ideal model delta sigma weight residual 1.497 1.435 0.062 1.40e-02 5.10e+03 1.93e+01 bond pdb=" CB HIS H 32 " pdb=" CG HIS H 32 " ideal model delta sigma weight residual 1.497 1.436 0.061 1.40e-02 5.10e+03 1.91e+01 bond pdb=" CA PHE A 53 " pdb=" C PHE A 53 " ideal model delta sigma weight residual 1.522 1.473 0.050 1.19e-02 7.06e+03 1.73e+01 bond pdb=" CA PHE D 53 " pdb=" C PHE D 53 " ideal model delta sigma weight residual 1.522 1.473 0.050 1.19e-02 7.06e+03 1.73e+01 ... (remaining 20371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 23849 2.42 - 4.84: 3222 4.84 - 7.26: 530 7.26 - 9.68: 53 9.68 - 12.10: 3 Bond angle restraints: 27657 Sorted by residual: angle pdb=" N LEU B 520 " pdb=" CA LEU B 520 " pdb=" C LEU B 520 " ideal model delta sigma weight residual 113.50 101.40 12.10 1.23e+00 6.61e-01 9.69e+01 angle pdb=" N LEU E 520 " pdb=" CA LEU E 520 " pdb=" C LEU E 520 " ideal model delta sigma weight residual 113.50 101.42 12.08 1.23e+00 6.61e-01 9.65e+01 angle pdb=" N LEU F 520 " pdb=" CA LEU F 520 " pdb=" C LEU F 520 " ideal model delta sigma weight residual 113.50 101.45 12.05 1.23e+00 6.61e-01 9.60e+01 angle pdb=" C CYS C 239 " pdb=" N PRO C 240 " pdb=" CA PRO C 240 " ideal model delta sigma weight residual 119.56 127.26 -7.70 1.02e+00 9.61e-01 5.69e+01 angle pdb=" C CYS D 239 " pdb=" N PRO D 240 " pdb=" CA PRO D 240 " ideal model delta sigma weight residual 119.56 127.24 -7.68 1.02e+00 9.61e-01 5.66e+01 ... (remaining 27652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.51: 12984 22.51 - 45.01: 366 45.01 - 67.52: 87 67.52 - 90.02: 63 90.02 - 112.53: 24 Dihedral angle restraints: 13524 sinusoidal: 6747 harmonic: 6777 Sorted by residual: dihedral pdb=" CA CYS D 126 " pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " ideal model delta sinusoidal sigma weight residual 79.00 5.72 73.28 1 2.00e+01 2.50e-03 1.71e+01 dihedral pdb=" CA CYS A 126 " pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " ideal model delta sinusoidal sigma weight residual 79.00 5.73 73.27 1 2.00e+01 2.50e-03 1.71e+01 dihedral pdb=" CA CYS C 126 " pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " ideal model delta sinusoidal sigma weight residual 79.00 5.75 73.25 1 2.00e+01 2.50e-03 1.71e+01 ... (remaining 13521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2473 0.106 - 0.212: 821 0.212 - 0.319: 86 0.319 - 0.425: 1 0.425 - 0.531: 6 Chirality restraints: 3387 Sorted by residual: chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.43e+01 chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.39e+01 chirality pdb=" C1 NAG p 2 " pdb=" O4 NAG p 1 " pdb=" C2 NAG p 2 " pdb=" O5 NAG p 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.29e+01 ... (remaining 3384 not shown) Planarity restraints: 3429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 611 " 0.076 2.00e-02 2.50e+03 7.95e-02 7.90e+01 pdb=" CG ASN E 611 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN E 611 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN E 611 " -0.124 2.00e-02 2.50e+03 pdb=" C1 NAG E 703 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 611 " 0.076 2.00e-02 2.50e+03 7.94e-02 7.89e+01 pdb=" CG ASN B 611 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN B 611 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN B 611 " -0.124 2.00e-02 2.50e+03 pdb=" C1 NAG B 703 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 611 " 0.076 2.00e-02 2.50e+03 7.94e-02 7.88e+01 pdb=" CG ASN F 611 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN F 611 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN F 611 " -0.124 2.00e-02 2.50e+03 pdb=" C1 NAG F 703 " 0.095 2.00e-02 2.50e+03 ... (remaining 3426 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5065 2.80 - 3.32: 17794 3.32 - 3.85: 33633 3.85 - 4.37: 39409 4.37 - 4.90: 63111 Nonbonded interactions: 159012 Sorted by model distance: nonbonded pdb=" O3 NAG M 1 " pdb=" O7 NAG M 1 " model vdw 2.270 3.040 nonbonded pdb=" O3 NAG i 1 " pdb=" O7 NAG i 1 " model vdw 2.270 3.040 nonbonded pdb=" O3 NAG X 1 " pdb=" O7 NAG X 1 " model vdw 2.270 3.040 nonbonded pdb=" N ASN A 355 " pdb=" OD1 ASN A 355 " model vdw 2.308 3.120 nonbonded pdb=" N ASN C 355 " pdb=" OD1 ASN C 355 " model vdw 2.308 3.120 ... (remaining 159007 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'X' selection = chain 'b' selection = chain 'i' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 45.240 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 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 : 0.018 0.105 20376 Z= 1.179 Angle : 1.760 12.105 27657 Z= 1.124 Chirality : 0.098 0.531 3387 Planarity : 0.009 0.049 3375 Dihedral : 12.940 112.525 9045 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.65 % Allowed : 2.86 % Favored : 96.49 % Rotamer: Outliers : 0.15 % Allowed : 1.02 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.70 (0.17), residues: 2310 helix: -0.39 (0.24), residues: 390 sheet: 1.07 (0.20), residues: 630 loop : 0.58 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.010 TRP E 571 HIS 0.017 0.004 HIS D 374 PHE 0.040 0.007 PHE E 522 TYR 0.060 0.009 TYR E 638 ARG 0.005 0.001 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 815 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8629 (mt) cc_final: 0.8167 (mm) REVERT: A 116 LEU cc_start: 0.8467 (mt) cc_final: 0.7952 (mt) REVERT: A 373 THR cc_start: 0.8850 (p) cc_final: 0.8389 (p) REVERT: A 450 THR cc_start: 0.8386 (p) cc_final: 0.7688 (t) REVERT: B 586 TYR cc_start: 0.9136 (t80) cc_final: 0.8526 (t80) REVERT: B 604 CYS cc_start: 0.5202 (t) cc_final: 0.4887 (t) REVERT: H 25 SER cc_start: 0.7152 (t) cc_final: 0.5102 (p) REVERT: L 10 PHE cc_start: 0.7351 (p90) cc_final: 0.7096 (p90) REVERT: L 92 ASN cc_start: 0.8912 (t0) cc_final: 0.8371 (t0) REVERT: C 52 LEU cc_start: 0.8588 (mt) cc_final: 0.8210 (mm) REVERT: C 116 LEU cc_start: 0.8643 (mt) cc_final: 0.8272 (mt) REVERT: C 217 TYR cc_start: 0.8203 (m-80) cc_final: 0.7581 (m-80) REVERT: C 251 ILE cc_start: 0.9410 (mt) cc_final: 0.9185 (tp) REVERT: C 373 THR cc_start: 0.8858 (p) cc_final: 0.8399 (p) REVERT: C 450 THR cc_start: 0.8362 (p) cc_final: 0.7672 (t) REVERT: E 584 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8508 (mt-10) REVERT: E 610 TRP cc_start: 0.8569 (t-100) cc_final: 0.8140 (t-100) REVERT: E 643 TYR cc_start: 0.8749 (m-10) cc_final: 0.8544 (m-80) REVERT: G 25 SER cc_start: 0.7059 (t) cc_final: 0.5131 (p) REVERT: J 10 PHE cc_start: 0.7430 (p90) cc_final: 0.7157 (p90) REVERT: D 42 VAL cc_start: 0.9486 (t) cc_final: 0.9286 (p) REVERT: D 52 LEU cc_start: 0.8583 (mt) cc_final: 0.8139 (mm) REVERT: D 107 ASP cc_start: 0.8614 (m-30) cc_final: 0.8379 (p0) REVERT: D 114 GLN cc_start: 0.8831 (tp40) cc_final: 0.8609 (tm-30) REVERT: D 217 TYR cc_start: 0.8344 (m-80) cc_final: 0.7421 (m-80) REVERT: D 373 THR cc_start: 0.8822 (p) cc_final: 0.8575 (p) REVERT: D 450 THR cc_start: 0.8213 (p) cc_final: 0.7535 (t) REVERT: F 543 ASN cc_start: 0.8871 (m-40) cc_final: 0.8595 (t0) REVERT: F 584 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8258 (mt-10) REVERT: I 25 SER cc_start: 0.6930 (t) cc_final: 0.4800 (p) REVERT: K 10 PHE cc_start: 0.7492 (p90) cc_final: 0.7255 (p90) REVERT: K 92 ASN cc_start: 0.8832 (t0) cc_final: 0.8583 (t0) outliers start: 3 outliers final: 3 residues processed: 818 average time/residue: 0.3212 time to fit residues: 398.9717 Evaluate side-chains 432 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 429 time to evaluate : 2.206 ------------------------------------------------------------------------------- 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: 0.9990 chunk 172 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 92 optimal weight: 0.0170 chunk 178 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 overall best weight: 0.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 550 GLN H 32 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 76 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 550 GLN ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 HIS G 35 HIS G 39 GLN J 76 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 HIS I 39 GLN K 76 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 20376 Z= 0.253 Angle : 0.813 9.559 27657 Z= 0.413 Chirality : 0.050 0.365 3387 Planarity : 0.005 0.035 3375 Dihedral : 8.668 63.808 4689 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.64 % Favored : 95.84 % Rotamer: Outliers : 0.05 % Allowed : 2.52 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.46 (0.17), residues: 2310 helix: 0.53 (0.27), residues: 390 sheet: 0.98 (0.19), residues: 675 loop : -0.07 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 610 HIS 0.010 0.002 HIS D 105 PHE 0.036 0.003 PHE K 71 TYR 0.027 0.002 TYR I 100I ARG 0.007 0.001 ARG D 151 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 601 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ILE cc_start: 0.9396 (tp) cc_final: 0.9109 (tt) REVERT: B 586 TYR cc_start: 0.8965 (t80) cc_final: 0.8374 (t80) REVERT: B 642 ILE cc_start: 0.9692 (mt) cc_final: 0.9354 (tt) REVERT: H 18 LEU cc_start: 0.8407 (tt) cc_final: 0.7391 (tt) REVERT: L 37 GLN cc_start: 0.8493 (pp30) cc_final: 0.8291 (pp30) REVERT: C 36 VAL cc_start: 0.9220 (t) cc_final: 0.9017 (t) REVERT: C 157 CYS cc_start: 0.6458 (m) cc_final: 0.6186 (m) REVERT: C 373 THR cc_start: 0.8982 (p) cc_final: 0.8726 (t) REVERT: E 545 LEU cc_start: 0.8930 (tp) cc_final: 0.8571 (tt) REVERT: E 584 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8335 (mt-10) REVERT: E 586 TYR cc_start: 0.9101 (t80) cc_final: 0.8048 (t80) REVERT: E 588 ARG cc_start: 0.9221 (ttp80) cc_final: 0.8985 (ttp80) REVERT: E 591 GLN cc_start: 0.9067 (tp40) cc_final: 0.8331 (tp40) REVERT: G 58 TYR cc_start: 0.8642 (m-10) cc_final: 0.8396 (m-10) REVERT: G 61 ASP cc_start: 0.8491 (p0) cc_final: 0.8195 (p0) REVERT: D 217 TYR cc_start: 0.8080 (m-80) cc_final: 0.7682 (m-80) REVERT: D 373 THR cc_start: 0.8996 (p) cc_final: 0.8724 (t) REVERT: F 543 ASN cc_start: 0.8572 (m-40) cc_final: 0.8316 (t0) REVERT: F 584 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8369 (mt-10) REVERT: F 639 THR cc_start: 0.9034 (p) cc_final: 0.8736 (p) REVERT: I 18 LEU cc_start: 0.8417 (tt) cc_final: 0.7209 (tt) REVERT: I 61 ASP cc_start: 0.8386 (p0) cc_final: 0.8180 (p0) REVERT: K 33 LEU cc_start: 0.8372 (tp) cc_final: 0.7912 (tp) REVERT: K 78 LEU cc_start: 0.9093 (tp) cc_final: 0.8854 (tp) outliers start: 1 outliers final: 0 residues processed: 601 average time/residue: 0.2727 time to fit residues: 260.1430 Evaluate side-chains 433 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 20.0000 chunk 64 optimal weight: 0.0980 chunk 172 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS J 6 GLN J 24 GLN ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN K 6 GLN K 24 GLN K 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 20376 Z= 0.240 Angle : 0.731 8.643 27657 Z= 0.369 Chirality : 0.046 0.297 3387 Planarity : 0.004 0.068 3375 Dihedral : 7.067 50.432 4689 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.42 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.35 (0.17), residues: 2310 helix: 0.58 (0.26), residues: 408 sheet: 0.83 (0.18), residues: 699 loop : -0.18 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 596 HIS 0.007 0.001 HIS A 105 PHE 0.023 0.002 PHE C 53 TYR 0.027 0.002 TYR E 586 ARG 0.008 0.001 ARG F 585 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 515 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.8384 (m-40) cc_final: 0.8141 (p0) REVERT: A 98 ASN cc_start: 0.8653 (t0) cc_final: 0.8436 (t0) REVERT: A 211 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7769 (tm-30) REVERT: B 543 ASN cc_start: 0.8502 (t0) cc_final: 0.8223 (t0) REVERT: B 642 ILE cc_start: 0.9705 (mt) cc_final: 0.9343 (tt) REVERT: H 18 LEU cc_start: 0.8479 (tt) cc_final: 0.8024 (tt) REVERT: H 27 PHE cc_start: 0.7633 (p90) cc_final: 0.7087 (p90) REVERT: H 51 ILE cc_start: 0.9318 (mt) cc_final: 0.9080 (pt) REVERT: H 100 TYR cc_start: 0.8283 (t80) cc_final: 0.7971 (t80) REVERT: E 545 LEU cc_start: 0.8686 (tp) cc_final: 0.8287 (tt) REVERT: E 591 GLN cc_start: 0.9150 (tp40) cc_final: 0.8806 (tp40) REVERT: E 632 ASP cc_start: 0.8708 (t70) cc_final: 0.8457 (t70) REVERT: E 642 ILE cc_start: 0.9689 (mt) cc_final: 0.9384 (tt) REVERT: G 18 LEU cc_start: 0.8433 (tt) cc_final: 0.7713 (tt) REVERT: G 51 ILE cc_start: 0.9276 (mt) cc_final: 0.8982 (pt) REVERT: G 58 TYR cc_start: 0.8757 (m-80) cc_final: 0.8293 (m-10) REVERT: D 211 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7587 (tm-30) REVERT: D 233 PHE cc_start: 0.8979 (t80) cc_final: 0.8711 (t80) REVERT: F 549 VAL cc_start: 0.7922 (m) cc_final: 0.7576 (t) REVERT: I 18 LEU cc_start: 0.8225 (tt) cc_final: 0.7761 (tt) REVERT: K 55 ILE cc_start: 0.9060 (mt) cc_final: 0.8806 (tp) REVERT: K 87 TYR cc_start: 0.8168 (m-80) cc_final: 0.7964 (m-80) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.2655 time to fit residues: 222.1353 Evaluate side-chains 394 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 394 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 208 optimal weight: 9.9990 chunk 220 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS L 24 GLN ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 20376 Z= 0.368 Angle : 0.780 12.019 27657 Z= 0.394 Chirality : 0.046 0.261 3387 Planarity : 0.005 0.059 3375 Dihedral : 6.584 59.630 4689 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.45 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.03 (0.17), residues: 2310 helix: 0.12 (0.25), residues: 438 sheet: 0.52 (0.18), residues: 726 loop : -0.34 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP G 100H HIS 0.005 0.001 HIS I 32 PHE 0.033 0.003 PHE A 53 TYR 0.027 0.002 TYR E 586 ARG 0.015 0.001 ARG E 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 468 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.8407 (m-40) cc_final: 0.8168 (p0) REVERT: A 256 SER cc_start: 0.8440 (p) cc_final: 0.8183 (p) REVERT: B 543 ASN cc_start: 0.8621 (t0) cc_final: 0.8332 (t0) REVERT: B 642 ILE cc_start: 0.9706 (mt) cc_final: 0.9410 (tt) REVERT: H 100 TYR cc_start: 0.8574 (t80) cc_final: 0.8320 (t80) REVERT: L 37 GLN cc_start: 0.8500 (pp30) cc_final: 0.8283 (pp30) REVERT: C 233 PHE cc_start: 0.8922 (t80) cc_final: 0.8681 (t80) REVERT: E 632 ASP cc_start: 0.8786 (t70) cc_final: 0.8543 (t70) REVERT: E 642 ILE cc_start: 0.9685 (mt) cc_final: 0.9387 (tt) REVERT: G 51 ILE cc_start: 0.9215 (mt) cc_final: 0.8981 (pt) REVERT: G 58 TYR cc_start: 0.8829 (m-80) cc_final: 0.8405 (m-10) REVERT: G 61 ASP cc_start: 0.8483 (p0) cc_final: 0.8266 (p0) REVERT: J 55 ILE cc_start: 0.8945 (mt) cc_final: 0.8607 (tp) REVERT: D 72 HIS cc_start: 0.7330 (m-70) cc_final: 0.6987 (m90) REVERT: D 173 TYR cc_start: 0.8365 (p90) cc_final: 0.8157 (p90) REVERT: D 260 LEU cc_start: 0.9185 (mt) cc_final: 0.8885 (mp) REVERT: D 434 MET cc_start: 0.8035 (mpp) cc_final: 0.7663 (mpp) REVERT: F 530 MET cc_start: 0.8703 (mtp) cc_final: 0.8180 (mtp) REVERT: F 642 ILE cc_start: 0.9674 (mt) cc_final: 0.9379 (tt) REVERT: K 92 ASN cc_start: 0.8774 (t0) cc_final: 0.8439 (t0) outliers start: 0 outliers final: 0 residues processed: 468 average time/residue: 0.2562 time to fit residues: 196.0456 Evaluate side-chains 353 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 188 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 20376 Z= 0.242 Angle : 0.697 10.199 27657 Z= 0.351 Chirality : 0.046 0.254 3387 Planarity : 0.004 0.050 3375 Dihedral : 6.141 57.635 4689 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.63 % Favored : 94.11 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.09 (0.17), residues: 2310 helix: 0.02 (0.25), residues: 444 sheet: 0.72 (0.19), residues: 666 loop : -0.49 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 69 HIS 0.006 0.001 HIS G 35 PHE 0.028 0.002 PHE B 522 TYR 0.025 0.002 TYR B 586 ARG 0.005 0.000 ARG E 585 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 443 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.8511 (m-40) cc_final: 0.8278 (p0) REVERT: B 642 ILE cc_start: 0.9713 (mt) cc_final: 0.9367 (tt) REVERT: H 27 PHE cc_start: 0.7952 (p90) cc_final: 0.7657 (p90) REVERT: C 67 ASN cc_start: 0.8629 (m-40) cc_final: 0.8399 (p0) REVERT: C 434 MET cc_start: 0.8116 (mpp) cc_final: 0.7895 (mpp) REVERT: E 543 ASN cc_start: 0.8360 (t0) cc_final: 0.8154 (t0) REVERT: E 632 ASP cc_start: 0.8708 (t70) cc_final: 0.8449 (t70) REVERT: E 642 ILE cc_start: 0.9694 (mt) cc_final: 0.9367 (tt) REVERT: G 51 ILE cc_start: 0.9184 (mt) cc_final: 0.8903 (pt) REVERT: G 58 TYR cc_start: 0.8817 (m-80) cc_final: 0.8452 (m-10) REVERT: G 61 ASP cc_start: 0.8461 (p0) cc_final: 0.8121 (t0) REVERT: J 55 ILE cc_start: 0.8972 (mt) cc_final: 0.8720 (tp) REVERT: D 116 LEU cc_start: 0.8526 (mt) cc_final: 0.8267 (mt) REVERT: F 530 MET cc_start: 0.8592 (mtp) cc_final: 0.8333 (mtp) REVERT: F 548 ILE cc_start: 0.8041 (tp) cc_final: 0.6964 (tp) REVERT: F 642 ILE cc_start: 0.9667 (mt) cc_final: 0.9374 (tt) outliers start: 0 outliers final: 0 residues processed: 443 average time/residue: 0.2512 time to fit residues: 185.7405 Evaluate side-chains 347 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 54 optimal weight: 0.0170 chunk 220 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 115 optimal weight: 8.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 HIS ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 20376 Z= 0.258 Angle : 0.709 11.322 27657 Z= 0.357 Chirality : 0.046 0.246 3387 Planarity : 0.005 0.084 3375 Dihedral : 6.077 55.710 4689 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.15 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.21 (0.18), residues: 2310 helix: 0.08 (0.25), residues: 438 sheet: 0.54 (0.19), residues: 699 loop : -0.58 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 69 HIS 0.003 0.001 HIS G 35 PHE 0.028 0.003 PHE I 91 TYR 0.021 0.002 TYR B 586 ARG 0.004 0.000 ARG E 585 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 427 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8580 (mt) cc_final: 0.8332 (mt) REVERT: B 530 MET cc_start: 0.8314 (mmp) cc_final: 0.7817 (mmt) REVERT: B 543 ASN cc_start: 0.8422 (t0) cc_final: 0.8212 (t0) REVERT: B 642 ILE cc_start: 0.9693 (mt) cc_final: 0.9393 (tt) REVERT: L 37 GLN cc_start: 0.8482 (pp30) cc_final: 0.8279 (pp30) REVERT: C 67 ASN cc_start: 0.8648 (m-40) cc_final: 0.8434 (p0) REVERT: C 116 LEU cc_start: 0.8520 (mt) cc_final: 0.8008 (mt) REVERT: E 543 ASN cc_start: 0.8659 (t0) cc_final: 0.8456 (t0) REVERT: E 598 CYS cc_start: 0.6501 (m) cc_final: 0.6269 (m) REVERT: E 632 ASP cc_start: 0.8752 (t70) cc_final: 0.8473 (t70) REVERT: E 642 ILE cc_start: 0.9682 (mt) cc_final: 0.9376 (tt) REVERT: G 18 LEU cc_start: 0.8304 (tt) cc_final: 0.7707 (tt) REVERT: G 35 HIS cc_start: 0.7553 (m90) cc_final: 0.7068 (m90) REVERT: G 58 TYR cc_start: 0.8820 (m-80) cc_final: 0.8513 (m-10) REVERT: G 61 ASP cc_start: 0.8536 (p0) cc_final: 0.8143 (t0) REVERT: D 72 HIS cc_start: 0.7271 (m-70) cc_final: 0.7011 (m90) REVERT: F 543 ASN cc_start: 0.8438 (t0) cc_final: 0.8233 (t0) REVERT: F 598 CYS cc_start: 0.6448 (m) cc_final: 0.6095 (m) REVERT: F 642 ILE cc_start: 0.9656 (mt) cc_final: 0.9381 (tt) REVERT: I 58 TYR cc_start: 0.8821 (m-80) cc_final: 0.8530 (m-10) REVERT: K 18 LYS cc_start: 0.9378 (mmtt) cc_final: 0.9176 (mmmt) REVERT: K 71 PHE cc_start: 0.8564 (m-80) cc_final: 0.7833 (m-10) outliers start: 0 outliers final: 0 residues processed: 427 average time/residue: 0.2518 time to fit residues: 178.6536 Evaluate side-chains 336 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 chunk 124 optimal weight: 0.5980 chunk 185 optimal weight: 8.9990 chunk 123 optimal weight: 0.7980 chunk 219 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 133 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.6418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 20376 Z= 0.296 Angle : 0.749 11.348 27657 Z= 0.374 Chirality : 0.049 0.486 3387 Planarity : 0.005 0.070 3375 Dihedral : 6.302 54.650 4689 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.67 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.17), residues: 2310 helix: 0.17 (0.26), residues: 414 sheet: 0.41 (0.19), residues: 666 loop : -0.89 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 69 HIS 0.006 0.001 HIS I 32 PHE 0.028 0.003 PHE C 53 TYR 0.028 0.002 TYR A 435 ARG 0.005 0.001 ARG E 617 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 2.494 Fit side-chains revert: symmetry clash REVERT: A 256 SER cc_start: 0.8564 (p) cc_final: 0.8350 (p) REVERT: B 520 LEU cc_start: 0.8706 (mm) cc_final: 0.8329 (mt) REVERT: B 530 MET cc_start: 0.8274 (mmp) cc_final: 0.7725 (mmt) REVERT: B 543 ASN cc_start: 0.8534 (t0) cc_final: 0.8111 (t0) REVERT: B 624 ASP cc_start: 0.9025 (p0) cc_final: 0.8809 (p0) REVERT: B 642 ILE cc_start: 0.9694 (mt) cc_final: 0.9396 (tt) REVERT: L 37 GLN cc_start: 0.8659 (pp30) cc_final: 0.8438 (pp30) REVERT: C 67 ASN cc_start: 0.8697 (m-40) cc_final: 0.8468 (p0) REVERT: E 595 ILE cc_start: 0.9646 (tp) cc_final: 0.9444 (tp) REVERT: E 632 ASP cc_start: 0.8776 (t70) cc_final: 0.8481 (t70) REVERT: E 642 ILE cc_start: 0.9686 (mt) cc_final: 0.9409 (tt) REVERT: G 35 HIS cc_start: 0.7599 (m90) cc_final: 0.7016 (m90) REVERT: G 61 ASP cc_start: 0.8585 (p0) cc_final: 0.8140 (t0) REVERT: D 53 PHE cc_start: 0.7679 (p90) cc_final: 0.7394 (p90) REVERT: F 520 LEU cc_start: 0.8576 (mm) cc_final: 0.8133 (mt) REVERT: F 543 ASN cc_start: 0.8539 (t0) cc_final: 0.8258 (t0) REVERT: F 598 CYS cc_start: 0.6339 (m) cc_final: 0.5936 (m) REVERT: F 642 ILE cc_start: 0.9643 (mt) cc_final: 0.9380 (tt) REVERT: K 18 LYS cc_start: 0.9334 (mmtt) cc_final: 0.9013 (mmmt) REVERT: K 71 PHE cc_start: 0.8575 (m-80) cc_final: 0.7961 (m-10) outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.2504 time to fit residues: 176.2106 Evaluate side-chains 327 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 131 optimal weight: 0.4980 chunk 66 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 139 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 172 optimal weight: 8.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 HIS ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.6738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 20376 Z= 0.292 Angle : 0.743 11.957 27657 Z= 0.371 Chirality : 0.048 0.423 3387 Planarity : 0.005 0.064 3375 Dihedral : 6.338 54.145 4689 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.84 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.51 (0.17), residues: 2310 helix: 0.28 (0.26), residues: 420 sheet: 0.35 (0.19), residues: 642 loop : -0.91 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 427 HIS 0.005 0.001 HIS C 249 PHE 0.027 0.003 PHE F 519 TYR 0.021 0.002 TYR F 586 ARG 0.006 0.001 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 421 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 SER cc_start: 0.8582 (p) cc_final: 0.8362 (p) REVERT: B 520 LEU cc_start: 0.8739 (mm) cc_final: 0.8392 (mt) REVERT: B 530 MET cc_start: 0.8356 (mmp) cc_final: 0.7812 (mmt) REVERT: B 543 ASN cc_start: 0.8540 (t0) cc_final: 0.8160 (t0) REVERT: B 642 ILE cc_start: 0.9694 (mt) cc_final: 0.9400 (tt) REVERT: L 37 GLN cc_start: 0.8692 (pp30) cc_final: 0.8442 (pp30) REVERT: E 642 ILE cc_start: 0.9677 (mt) cc_final: 0.9414 (tt) REVERT: G 61 ASP cc_start: 0.8519 (p0) cc_final: 0.8067 (t0) REVERT: J 53 GLN cc_start: 0.8677 (tp-100) cc_final: 0.8467 (tp-100) REVERT: F 543 ASN cc_start: 0.8571 (t0) cc_final: 0.8156 (t0) REVERT: F 548 ILE cc_start: 0.9382 (mm) cc_final: 0.9005 (mm) REVERT: F 598 CYS cc_start: 0.6250 (m) cc_final: 0.5754 (m) REVERT: F 642 ILE cc_start: 0.9640 (mt) cc_final: 0.9374 (tt) REVERT: I 34 MET cc_start: 0.8686 (mmp) cc_final: 0.8464 (mmp) REVERT: I 80 LEU cc_start: 0.8480 (tp) cc_final: 0.7676 (tp) REVERT: K 71 PHE cc_start: 0.8572 (m-80) cc_final: 0.8045 (m-10) outliers start: 0 outliers final: 0 residues processed: 421 average time/residue: 0.2461 time to fit residues: 171.4374 Evaluate side-chains 327 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 0.9990 chunk 210 optimal weight: 9.9990 chunk 192 optimal weight: 8.9990 chunk 204 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 160 optimal weight: 0.3980 chunk 62 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 195 ASN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.6890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 20376 Z= 0.198 Angle : 0.679 10.680 27657 Z= 0.339 Chirality : 0.047 0.353 3387 Planarity : 0.004 0.060 3375 Dihedral : 6.019 53.089 4689 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.75 % Favored : 92.90 % Rotamer: Outliers : 0.05 % Allowed : 0.44 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.47 (0.17), residues: 2310 helix: 0.54 (0.26), residues: 402 sheet: 0.35 (0.19), residues: 648 loop : -0.95 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 427 HIS 0.003 0.001 HIS D 374 PHE 0.038 0.002 PHE E 519 TYR 0.031 0.002 TYR D 217 ARG 0.004 0.000 ARG E 585 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 436 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 520 LEU cc_start: 0.8558 (mm) cc_final: 0.8202 (mt) REVERT: B 530 MET cc_start: 0.8277 (mmp) cc_final: 0.7735 (mmt) REVERT: B 543 ASN cc_start: 0.8568 (t0) cc_final: 0.8287 (t0) REVERT: B 624 ASP cc_start: 0.9124 (p0) cc_final: 0.8829 (p0) REVERT: B 626 MET cc_start: 0.8784 (mmp) cc_final: 0.8415 (mmm) REVERT: B 642 ILE cc_start: 0.9691 (mt) cc_final: 0.9394 (tt) REVERT: H 61 ASP cc_start: 0.8472 (p0) cc_final: 0.8011 (t0) REVERT: L 37 GLN cc_start: 0.8685 (pp30) cc_final: 0.8460 (pp30) REVERT: E 642 ILE cc_start: 0.9673 (mt) cc_final: 0.9381 (tt) REVERT: G 35 HIS cc_start: 0.7624 (m90) cc_final: 0.7224 (m90) REVERT: G 61 ASP cc_start: 0.8426 (p0) cc_final: 0.8100 (t0) REVERT: F 543 ASN cc_start: 0.8484 (t0) cc_final: 0.8071 (t0) REVERT: F 598 CYS cc_start: 0.6242 (m) cc_final: 0.5783 (m) REVERT: F 642 ILE cc_start: 0.9648 (mt) cc_final: 0.9382 (tt) REVERT: I 80 LEU cc_start: 0.8606 (tp) cc_final: 0.8036 (tp) REVERT: K 37 GLN cc_start: 0.8674 (pp30) cc_final: 0.8473 (pp30) REVERT: K 71 PHE cc_start: 0.8566 (m-80) cc_final: 0.8005 (m-10) REVERT: K 87 TYR cc_start: 0.8332 (m-80) cc_final: 0.7978 (m-80) outliers start: 1 outliers final: 0 residues processed: 437 average time/residue: 0.2551 time to fit residues: 184.8666 Evaluate side-chains 344 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 227 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 139 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS L 6 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.7039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20376 Z= 0.194 Angle : 0.678 11.111 27657 Z= 0.339 Chirality : 0.047 0.331 3387 Planarity : 0.004 0.057 3375 Dihedral : 5.823 52.813 4689 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.84 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.46 (0.17), residues: 2310 helix: 0.46 (0.26), residues: 420 sheet: 0.48 (0.20), residues: 615 loop : -0.97 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 427 HIS 0.012 0.001 HIS G 35 PHE 0.020 0.002 PHE G 100J TYR 0.018 0.001 TYR F 586 ARG 0.003 0.000 ARG E 585 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 437 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 520 LEU cc_start: 0.8600 (mm) cc_final: 0.8219 (mt) REVERT: B 530 MET cc_start: 0.8174 (mmp) cc_final: 0.7681 (mmt) REVERT: B 537 LEU cc_start: 0.9380 (mt) cc_final: 0.9172 (mm) REVERT: B 543 ASN cc_start: 0.8532 (t0) cc_final: 0.8263 (t0) REVERT: B 624 ASP cc_start: 0.9118 (p0) cc_final: 0.8814 (p0) REVERT: B 626 MET cc_start: 0.8748 (mmp) cc_final: 0.8372 (mmm) REVERT: B 642 ILE cc_start: 0.9694 (mt) cc_final: 0.9397 (tt) REVERT: H 49 SER cc_start: 0.7537 (p) cc_final: 0.7069 (t) REVERT: H 61 ASP cc_start: 0.8435 (p0) cc_final: 0.7922 (t0) REVERT: E 642 ILE cc_start: 0.9675 (mt) cc_final: 0.9410 (tt) REVERT: G 33 ASP cc_start: 0.7512 (p0) cc_final: 0.6704 (p0) REVERT: G 49 SER cc_start: 0.7971 (p) cc_final: 0.7695 (t) REVERT: G 61 ASP cc_start: 0.8394 (p0) cc_final: 0.8041 (t0) REVERT: J 53 GLN cc_start: 0.8672 (tp-100) cc_final: 0.8282 (tp-100) REVERT: D 256 SER cc_start: 0.8199 (m) cc_final: 0.7750 (m) REVERT: F 543 ASN cc_start: 0.8529 (t0) cc_final: 0.8213 (t0) REVERT: F 598 CYS cc_start: 0.5888 (m) cc_final: 0.5370 (m) REVERT: F 642 ILE cc_start: 0.9628 (mt) cc_final: 0.9366 (tt) REVERT: I 49 SER cc_start: 0.7577 (p) cc_final: 0.7354 (t) REVERT: I 80 LEU cc_start: 0.8583 (tp) cc_final: 0.7755 (tp) REVERT: I 100 TYR cc_start: 0.8189 (t80) cc_final: 0.7982 (t80) REVERT: K 16 LYS cc_start: 0.9204 (mmpt) cc_final: 0.8994 (mmpt) REVERT: K 18 LYS cc_start: 0.9278 (mmtt) cc_final: 0.9009 (mmmt) REVERT: K 37 GLN cc_start: 0.8710 (pp30) cc_final: 0.8451 (pp30) REVERT: K 71 PHE cc_start: 0.8532 (m-80) cc_final: 0.8076 (m-10) REVERT: K 87 TYR cc_start: 0.8317 (m-80) cc_final: 0.7929 (m-80) outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.2475 time to fit residues: 180.5891 Evaluate side-chains 341 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 181 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.065823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.053256 restraints weight = 78272.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.055285 restraints weight = 43228.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.056753 restraints weight = 28576.577| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.7250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 20376 Z= 0.310 Angle : 0.742 8.611 27657 Z= 0.376 Chirality : 0.048 0.318 3387 Planarity : 0.005 0.055 3375 Dihedral : 6.051 57.352 4689 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.71 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.17), residues: 2310 helix: 0.28 (0.25), residues: 429 sheet: 0.35 (0.20), residues: 615 loop : -1.17 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP G 100H HIS 0.007 0.001 HIS G 35 PHE 0.023 0.002 PHE L 71 TYR 0.026 0.002 TYR A 217 ARG 0.004 0.001 ARG A 480 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4366.81 seconds wall clock time: 79 minutes 0.90 seconds (4740.90 seconds total)