Starting phenix.real_space_refine on Fri Sep 27 23:52:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtd_36641/09_2024/8jtd_36641.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtd_36641/09_2024/8jtd_36641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtd_36641/09_2024/8jtd_36641.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtd_36641/09_2024/8jtd_36641.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtd_36641/09_2024/8jtd_36641.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtd_36641/09_2024/8jtd_36641.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 36 atoms to isotropic. 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 111 5.16 5 C 10755 2.51 5 N 2830 2.21 5 O 3579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17275 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3545 Classifications: {'peptide': 450} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 426} Chain breaks: 2 Chain: "B" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "C" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Chain: "D" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3562 Classifications: {'peptide': 452} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "E" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "J" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1094 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "N" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" 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: "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: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "0" 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: "1" 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: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "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 Residues with excluded nonbonded symmetry interactions: 63 residue: pdb=" C1 NAG P 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG P 1 " occ=0.00 residue: pdb=" C1 NAG P 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG P 2 " occ=0.00 residue: pdb=" C1 NAG R 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG R 1 " occ=0.00 residue: pdb=" C1 NAG R 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG R 2 " occ=0.00 residue: pdb=" C1 NAG S 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG S 1 " occ=0.00 residue: pdb=" C1 NAG S 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG S 2 " occ=0.00 residue: pdb=" C1 BMA S 3 " occ=0.00 ... (9 atoms not shown) pdb=" O6 BMA S 3 " occ=0.00 residue: pdb=" C1 NAG T 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG T 1 " occ=0.00 residue: pdb=" C1 NAG T 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG T 2 " occ=0.00 residue: pdb=" C1 BMA T 3 " occ=0.00 ... (9 atoms not shown) pdb=" O6 BMA T 3 " occ=0.00 residue: pdb=" C1 MAN T 4 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN T 4 " occ=0.00 residue: pdb=" C1 MAN T 5 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN T 5 " occ=0.00 ... (remaining 51 not shown) Time building chain proxies: 9.92, per 1000 atoms: 0.57 Number of scatterers: 17275 At special positions: 0 Unit cell: (129, 137.6, 166.84, 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 111 16.00 O 3579 8.00 N 2830 7.00 C 10755 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 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=2.03 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=2.03 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 F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS D 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=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS E 605 " distance=2.04 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 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 Atom "HETATM17035 O5 NAG A 603 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN T 4 " - " MAN T 5 " " MAN f 4 " - " MAN f 5 " " MAN q 4 " - " MAN q 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA T 3 " - " MAN T 4 " " BMA Y 3 " - " MAN Y 4 " " BMA f 3 " - " MAN f 4 " " MAN f 6 " - " MAN f 7 " " BMA k 3 " - " MAN k 4 " " BMA q 3 " - " MAN q 4 " " MAN q 6 " - " MAN q 7 " " BMA s 3 " - " MAN s 4 " " MAN s 6 " - " MAN s 7 " " BMA x 3 " - " MAN x 4 " ALPHA1-6 " BMA T 3 " - " MAN T 6 " " BMA Y 3 " - " MAN Y 5 " " BMA f 3 " - " MAN f 6 " " BMA k 3 " - " MAN k 5 " " BMA q 3 " - " MAN q 6 " " MAN q 6 " - " MAN q 8 " " BMA s 3 " - " MAN s 6 " " BMA x 3 " - " MAN x 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " 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 Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG 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 s 2 " - " BMA s 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " NAG-ASN " NAG 0 1 " - " ASN E 637 " " NAG 1 1 " - " ASN F 611 " " NAG A 601 " - " ASN A 234 " " NAG A 602 " - " ASN A 339 " " NAG A 603 " - " ASN A 355 " " NAG A 604 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 339 " " NAG C 604 " - " ASN C 355 " " NAG D 601 " - " ASN D 133 " " NAG D 602 " - " ASN D 234 " " NAG D 603 " - " ASN D 339 " " NAG D 604 " - " ASN D 355 " " NAG D 605 " - " ASN D 392 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 618 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG O 1 " - " ASN A 88 " " NAG P 1 " - " ASN A 133 " " NAG Q 1 " - " ASN A 156 " " NAG R 1 " - " ASN A 160 " " NAG S 1 " - " ASN A 197 " " NAG T 1 " - " ASN A 262 " " NAG V 1 " - " ASN A 295 " " NAG W 1 " - " ASN A 301 " " NAG X 1 " - " ASN A 332 " " NAG Y 1 " - " ASN A 363 " " NAG Z 1 " - " ASN A 386 " " NAG a 1 " - " ASN A 448 " " NAG b 1 " - " ASN C 133 " " NAG c 1 " - " ASN C 156 " " NAG d 1 " - " ASN C 160 " " NAG e 1 " - " ASN C 197 " " NAG f 1 " - " ASN C 262 " " NAG h 1 " - " ASN C 295 " " NAG i 1 " - " ASN C 301 " " NAG j 1 " - " ASN C 332 " " NAG k 1 " - " ASN C 363 " " NAG l 1 " - " ASN C 386 " " NAG m 1 " - " ASN C 392 " " NAG n 1 " - " ASN C 448 " " NAG o 1 " - " ASN D 88 " " NAG p 1 " - " ASN D 156 " " NAG q 1 " - " ASN D 160 " " NAG r 1 " - " ASN D 197 " " NAG s 1 " - " ASN D 262 " " NAG u 1 " - " ASN D 295 " " NAG v 1 " - " ASN D 301 " " NAG w 1 " - " ASN D 332 " " NAG x 1 " - " ASN D 363 " " NAG y 1 " - " ASN D 386 " " NAG z 1 " - " ASN D 448 " Time building additional restraints: 6.06 Conformation dependent library (CDL) restraints added in 1.9 seconds 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3686 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 33 sheets defined 27.1% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 59 through 64 removed outlier: 3.695A pdb=" N THR A 63 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.646A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 475 through 484 removed outlier: 4.654A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 removed outlier: 3.654A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.422A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 597 Processing helix chain 'B' and resid 611 through 615 removed outlier: 3.841A pdb=" N SER B 615 " --> pdb=" O SER B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 removed outlier: 4.219A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.886A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLN B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 removed outlier: 3.922A pdb=" N THR C 63 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.927A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C 127 " --> pdb=" O PRO C 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 127' Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 377 through 381 removed outlier: 3.667A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 392 Processing helix chain 'C' and resid 460 through 464 removed outlier: 3.682A pdb=" N SER C 463 " --> pdb=" O SER C 460 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR C 464 " --> pdb=" O THR C 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 460 through 464' Processing helix chain 'C' and resid 475 through 484 Processing helix chain 'D' and resid 59 through 64 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 removed outlier: 3.505A pdb=" N ARG D 151 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 335 through 350 Processing helix chain 'D' and resid 351 through 353 No H-bonds generated for 'chain 'D' and resid 351 through 353' Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 377 through 381 removed outlier: 3.668A pdb=" N GLU D 381 " --> pdb=" O CYS D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 392 removed outlier: 3.660A pdb=" N PHE D 391 " --> pdb=" O SER D 388 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN D 392 " --> pdb=" O GLY D 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 388 through 392' Processing helix chain 'D' and resid 474 through 484 removed outlier: 3.918A pdb=" N ASN D 478 " --> pdb=" O ASP D 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 removed outlier: 3.705A pdb=" N ALA E 526 " --> pdb=" O LEU E 523 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 535 removed outlier: 3.954A pdb=" N MET E 535 " --> pdb=" O ALA E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 543 removed outlier: 4.303A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 596 Processing helix chain 'E' and resid 618 through 624 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 649 Processing helix chain 'E' and resid 650 through 664 removed outlier: 3.728A pdb=" N ASP E 664 " --> pdb=" O LEU E 660 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 3.614A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 removed outlier: 3.882A pdb=" N SER F 534 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 531 through 535' Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.170A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 597 Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 650 removed outlier: 4.111A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 664 removed outlier: 3.596A pdb=" N ASP F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 31 removed outlier: 5.831A pdb=" N PHE J 29 " --> pdb=" O GLY J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 62 removed outlier: 3.791A pdb=" N GLN J 62 " --> pdb=" O GLN J 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 59 through 62' Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.603A pdb=" N VAL N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.655A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS A 218 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ILE A 215 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY A 250 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR A 217 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.120A pdb=" N ILE A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A 244 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.691A pdb=" N VAL A 172 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 159 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 130 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.404A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 9.769A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 10.945A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.414A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.945A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.769A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A 361 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AB2, first strand: chain 'C' and resid 46 through 47 removed outlier: 3.632A pdb=" N VAL C 489 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 224 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.179A pdb=" N GLN C 130 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.853A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.032A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.085A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.016A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.050A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS C 331 " --> pdb=" O LEU C 416 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 416 " --> pdb=" O CYS C 331 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 333 " --> pdb=" O ILE C 414 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE C 376 " --> pdb=" O PHE C 383 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.050A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.016A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.085A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.032A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE C 361 " --> pdb=" O SER C 393 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AB9, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AC1, first strand: chain 'D' and resid 494 through 499 Processing sheet with id=AC2, first strand: chain 'D' and resid 76 through 77 removed outlier: 7.381A pdb=" N THR D 77 " --> pdb=" O CYS D 54 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER D 56 " --> pdb=" O THR D 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 84 through 86 removed outlier: 4.302A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA D 224 " --> pdb=" O VAL D 489 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL D 489 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS D 487 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 177 removed outlier: 3.700A pdb=" N MET D 161 " --> pdb=" O GLN D 170 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL D 172 " --> pdb=" O PHE D 159 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE D 159 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN D 156 " --> pdb=" O THR D 132 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 202 through 203 removed outlier: 6.843A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.521A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.521A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 359 " --> pdb=" O TRP D 395 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 374 through 376 removed outlier: 3.900A pdb=" N HIS D 330 " --> pdb=" O THR D 297 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR D 297 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN D 295 " --> pdb=" O ASN D 332 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 304 through 308 Processing sheet with id=AD2, first strand: chain 'J' and resid 4 through 6 removed outlier: 5.814A pdb=" N SER J 16 " --> pdb=" O GLY J 82B" (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU J 81 " --> pdb=" O THR J 68 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.168A pdb=" N GLU J 10 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.168A pdb=" N GLU J 10 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N CYS J 92 " --> pdb=" O TRP J 108 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N TRP J 108 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR J 94 " --> pdb=" O ASP J 106 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N HIS J 98 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU J 102 " --> pdb=" O HIS J 98 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU J 100 " --> pdb=" O ASP J 100R" (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASP J 100R" --> pdb=" O LEU J 100 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ASP J 100B" --> pdb=" O TRP J 100P" (cutoff:3.500A) removed outlier: 7.580A pdb=" N TRP J 100P" --> pdb=" O ASP J 100B" (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE J 100D" --> pdb=" O GLU J 100N" (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU J 100N" --> pdb=" O PHE J 100D" (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 4 through 7 removed outlier: 5.139A pdb=" N GLU N 17 " --> pdb=" O ARG N 77 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG N 77 " --> pdb=" O GLU N 17 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.509A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS N 53 " --> pdb=" O HIS N 49 " (cutoff:3.500A) 587 hydrogen bonds defined for protein. 1542 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: 5.61 Time building geometry restraints manager: 6.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5323 1.34 - 1.47: 4536 1.47 - 1.60: 7588 1.60 - 1.73: 0 1.73 - 1.85: 151 Bond restraints: 17598 Sorted by residual: bond pdb=" C1 NAG D 603 " pdb=" O5 NAG D 603 " ideal model delta sigma weight residual 1.406 1.506 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C1 NAG A 603 " pdb=" O5 NAG A 603 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C1 NAG B 703 " pdb=" O5 NAG B 703 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C1 NAG l 1 " pdb=" O5 NAG l 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.73e+00 bond pdb=" C1 NAG A 604 " pdb=" O5 NAG A 604 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.07e+00 ... (remaining 17593 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 23207 2.53 - 5.06: 586 5.06 - 7.59: 88 7.59 - 10.12: 6 10.12 - 12.65: 3 Bond angle restraints: 23890 Sorted by residual: angle pdb=" C LYS C 65 " pdb=" N HIS C 66 " pdb=" CA HIS C 66 " ideal model delta sigma weight residual 121.70 134.35 -12.65 1.80e+00 3.09e-01 4.94e+01 angle pdb=" CA ASN A 355 " pdb=" CB ASN A 355 " pdb=" CG ASN A 355 " ideal model delta sigma weight residual 112.60 118.14 -5.54 1.00e+00 1.00e+00 3.06e+01 angle pdb=" C LYS A 65 " pdb=" N HIS A 66 " pdb=" CA HIS A 66 " ideal model delta sigma weight residual 121.70 131.26 -9.56 1.80e+00 3.09e-01 2.82e+01 angle pdb=" C TRP A 427 " pdb=" CA TRP A 427 " pdb=" CB TRP A 427 " ideal model delta sigma weight residual 115.79 109.67 6.12 1.19e+00 7.06e-01 2.65e+01 angle pdb=" N ALA D 362 " pdb=" CA ALA D 362 " pdb=" C ALA D 362 " ideal model delta sigma weight residual 108.24 114.96 -6.72 1.32e+00 5.74e-01 2.59e+01 ... (remaining 23885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.62: 11370 24.62 - 49.24: 610 49.24 - 73.87: 110 73.87 - 98.49: 78 98.49 - 123.11: 49 Dihedral angle restraints: 12217 sinusoidal: 6513 harmonic: 5704 Sorted by residual: dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 5.43 87.57 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -6.88 -79.12 1 1.00e+01 1.00e-02 7.79e+01 dihedral pdb=" CA CYS C 385 " pdb=" C CYS C 385 " pdb=" N ASN C 386 " pdb=" CA ASN C 386 " ideal model delta harmonic sigma weight residual -180.00 -137.97 -42.03 0 5.00e+00 4.00e-02 7.07e+01 ... (remaining 12214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.226: 3040 0.226 - 0.451: 23 0.451 - 0.677: 4 0.677 - 0.902: 2 0.902 - 1.128: 1 Chirality restraints: 3070 Sorted by residual: chirality pdb=" C1 NAG s 1 " pdb=" ND2 ASN D 262 " pdb=" C2 NAG s 1 " pdb=" O5 NAG s 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.27 -1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN A 301 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN A 262 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.26e+01 ... (remaining 3067 not shown) Planarity restraints: 2917 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 355 " 0.083 2.00e-02 2.50e+03 7.33e-02 6.71e+01 pdb=" CG ASN A 355 " -0.085 2.00e-02 2.50e+03 pdb=" OD1 ASN A 355 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 355 " -0.073 2.00e-02 2.50e+03 pdb=" C1 NAG A 603 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 637 " -0.007 2.00e-02 2.50e+03 4.88e-02 2.97e+01 pdb=" CG ASN B 637 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN B 637 " -0.057 2.00e-02 2.50e+03 pdb=" ND2 ASN B 637 " 0.054 2.00e-02 2.50e+03 pdb=" C1 NAG B 703 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 339 " 0.005 2.00e-02 2.50e+03 4.68e-02 2.74e+01 pdb=" CG ASN D 339 " -0.072 2.00e-02 2.50e+03 pdb=" OD1 ASN D 339 " 0.057 2.00e-02 2.50e+03 pdb=" ND2 ASN D 339 " -0.030 2.00e-02 2.50e+03 pdb=" C1 NAG D 603 " 0.040 2.00e-02 2.50e+03 ... (remaining 2914 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 360 2.62 - 3.19: 16069 3.19 - 3.76: 27137 3.76 - 4.33: 35865 4.33 - 4.90: 56131 Nonbonded interactions: 135562 Sorted by model distance: nonbonded pdb=" O ILE F 595 " pdb=" ND2 ASN F 651 " model vdw 2.048 3.120 nonbonded pdb=" O ILE C 491 " pdb=" NH2 ARG F 585 " model vdw 2.068 3.120 nonbonded pdb=" OE1 GLU C 102 " pdb=" NH1 ARG C 476 " model vdw 2.168 3.120 nonbonded pdb=" OG1 THR J 83 " pdb=" OD1 ASP J 85 " model vdw 2.184 3.040 nonbonded pdb=" OG1 THR J 70 " pdb=" O TYR J 79 " model vdw 2.185 3.040 ... (remaining 135557 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 '0' selection = chain '1' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'z' } ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 32 through 398 or resid 412 through 506 or resid 601 throu \ gh 604)) selection = (chain 'D' and (resid 32 through 185 or resid 189 through 398 or resid 412 throu \ gh 506 or resid 601 through 604)) } ncs_group { reference = (chain 'B' and (resid 520 through 545 or resid 569 through 664 or resid 701 thro \ ugh 702)) selection = (chain 'E' and (resid 520 through 545 or resid 569 through 664 or resid 701 thro \ ugh 702)) selection = (chain 'F' and (resid 520 through 545 or resid 569 through 664 or resid 701 thro \ ugh 702)) } ncs_group { reference = chain 'S' selection = chain 'X' selection = chain 'd' selection = chain 'l' selection = chain 'y' } ncs_group { reference = (chain 'T' and (resid 1 or resid 4 through 6)) selection = (chain 'f' and (resid 2 or resid 5 through 7)) selection = (chain 's' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'Y' selection = chain 'k' selection = chain 'x' } 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=0.00 max=1.00 mean=0.95 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 39.840 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5552 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 : 0.005 0.100 17598 Z= 0.326 Angle : 0.930 12.649 23890 Z= 0.443 Chirality : 0.067 1.128 3070 Planarity : 0.004 0.054 2860 Dihedral : 17.494 123.110 8426 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.81 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.29 (0.19), residues: 1944 helix: 0.11 (0.26), residues: 418 sheet: 0.00 (0.22), residues: 509 loop : -0.31 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP D 45 HIS 0.007 0.001 HIS N 53 PHE 0.041 0.002 PHE D 288 TYR 0.030 0.002 TYR F 643 ARG 0.010 0.000 ARG F 585 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 1.839 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: A 66 HIS cc_start: 0.7063 (p-80) cc_final: 0.6635 (p-80) REVERT: A 108 ILE cc_start: 0.8499 (mp) cc_final: 0.7595 (mp) REVERT: A 190 GLU cc_start: 0.6156 (pm20) cc_final: 0.5276 (pm20) REVERT: C 271 MET cc_start: 0.4814 (tpt) cc_final: 0.4506 (mmm) REVERT: C 298 ARG cc_start: 0.7662 (tmm-80) cc_final: 0.7314 (tmm-80) REVERT: C 423 ILE cc_start: 0.7945 (mt) cc_final: 0.7674 (mt) REVERT: D 216 HIS cc_start: 0.6996 (m-70) cc_final: 0.6430 (m170) REVERT: D 318 TYR cc_start: 0.7514 (m-10) cc_final: 0.7118 (m-80) REVERT: D 391 PHE cc_start: 0.7661 (m-80) cc_final: 0.7394 (m-80) REVERT: D 434 MET cc_start: 0.5241 (ptm) cc_final: 0.4438 (ppp) REVERT: D 484 TYR cc_start: 0.7944 (p90) cc_final: 0.7482 (p90) REVERT: F 590 GLN cc_start: 0.8914 (tt0) cc_final: 0.8446 (pt0) REVERT: F 601 LYS cc_start: 0.7682 (mppt) cc_final: 0.7429 (mmtm) REVERT: F 643 TYR cc_start: 0.8122 (m-80) cc_final: 0.7676 (m-80) REVERT: F 656 ASN cc_start: 0.9130 (t0) cc_final: 0.8889 (t0) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.2840 time to fit residues: 160.6477 Evaluate side-chains 299 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 153 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN A 428 GLN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN C 72 HIS ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 GLN E 540 GLN E 651 ASN F 540 GLN F 575 GLN F 591 GLN F 650 GLN J 32 HIS ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 HIS ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5594 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17598 Z= 0.220 Angle : 0.762 11.551 23890 Z= 0.377 Chirality : 0.054 0.832 3070 Planarity : 0.005 0.061 2860 Dihedral : 14.946 110.289 4728 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.34 % Allowed : 5.28 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.18), residues: 1944 helix: 0.14 (0.26), residues: 424 sheet: -0.03 (0.21), residues: 512 loop : -0.47 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 45 HIS 0.006 0.001 HIS N 53 PHE 0.021 0.002 PHE C 159 TYR 0.026 0.002 TYR F 643 ARG 0.015 0.001 ARG E 585 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 383 time to evaluate : 1.666 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: A 66 HIS cc_start: 0.7163 (p-80) cc_final: 0.6854 (p-80) REVERT: A 104 MET cc_start: 0.8207 (tpt) cc_final: 0.7935 (tpp) REVERT: A 108 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.7500 (mp) REVERT: A 190 GLU cc_start: 0.6672 (pm20) cc_final: 0.5746 (pm20) REVERT: A 271 MET cc_start: -0.3867 (ttt) cc_final: -0.4143 (ttt) REVERT: A 423 ILE cc_start: 0.7745 (mm) cc_final: 0.7479 (mm) REVERT: C 271 MET cc_start: 0.5345 (tpt) cc_final: 0.5073 (mmm) REVERT: C 288 PHE cc_start: 0.7721 (m-10) cc_final: 0.7207 (m-80) REVERT: C 298 ARG cc_start: 0.8159 (tmm-80) cc_final: 0.7725 (tmm-80) REVERT: C 423 ILE cc_start: 0.8011 (mt) cc_final: 0.7712 (mt) REVERT: C 434 MET cc_start: 0.5348 (tmm) cc_final: 0.4137 (ttm) REVERT: D 216 HIS cc_start: 0.7316 (m-70) cc_final: 0.6896 (m170) REVERT: D 271 MET cc_start: 0.5906 (tmm) cc_final: 0.4443 (ttt) REVERT: D 342 LEU cc_start: 0.9008 (mp) cc_final: 0.8758 (mt) REVERT: D 391 PHE cc_start: 0.7829 (m-80) cc_final: 0.7575 (m-80) REVERT: E 545 LEU cc_start: 0.8893 (tp) cc_final: 0.8676 (tp) REVERT: F 588 ARG cc_start: 0.8035 (mmt180) cc_final: 0.7654 (mmt180) REVERT: F 591 GLN cc_start: 0.9170 (mt0) cc_final: 0.8790 (mt0) REVERT: F 601 LYS cc_start: 0.7845 (mppt) cc_final: 0.7625 (mmtm) REVERT: F 606 THR cc_start: 0.8399 (m) cc_final: 0.8184 (m) REVERT: F 643 TYR cc_start: 0.8323 (m-80) cc_final: 0.7899 (m-80) REVERT: J 45 LEU cc_start: 0.8089 (tp) cc_final: 0.7526 (tp) REVERT: J 48 MET cc_start: 0.7135 (mtm) cc_final: 0.6807 (mtm) REVERT: J 70 THR cc_start: 0.8956 (p) cc_final: 0.8704 (p) outliers start: 6 outliers final: 2 residues processed: 386 average time/residue: 0.2878 time to fit residues: 168.6519 Evaluate side-chains 307 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 304 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 176 optimal weight: 0.0030 chunk 60 optimal weight: 0.0370 chunk 143 optimal weight: 9.9990 overall best weight: 0.5872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN C 195 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN F 540 GLN ** J 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN N 53 HIS ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5544 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17598 Z= 0.182 Angle : 0.727 10.575 23890 Z= 0.356 Chirality : 0.053 0.784 3070 Planarity : 0.004 0.056 2860 Dihedral : 12.996 111.011 4728 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.34 % Allowed : 3.16 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.19), residues: 1944 helix: 0.36 (0.27), residues: 424 sheet: 0.10 (0.21), residues: 516 loop : -0.44 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 45 HIS 0.007 0.001 HIS A 216 PHE 0.022 0.002 PHE C 159 TYR 0.025 0.001 TYR F 643 ARG 0.006 0.000 ARG E 588 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 403 time to evaluate : 1.872 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: A 66 HIS cc_start: 0.7748 (p-80) cc_final: 0.7466 (p-80) REVERT: A 94 ASN cc_start: 0.9225 (t0) cc_final: 0.9008 (t0) REVERT: A 104 MET cc_start: 0.8201 (tpt) cc_final: 0.7873 (tpp) REVERT: A 108 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.7412 (mp) REVERT: A 190 GLU cc_start: 0.6583 (pm20) cc_final: 0.6056 (pm20) REVERT: A 216 HIS cc_start: 0.8034 (m-70) cc_final: 0.7703 (m-70) REVERT: A 384 TYR cc_start: 0.6649 (m-80) cc_final: 0.6287 (m-80) REVERT: A 423 ILE cc_start: 0.7737 (mm) cc_final: 0.7440 (mm) REVERT: B 588 ARG cc_start: 0.9034 (mtt180) cc_final: 0.8679 (ttm170) REVERT: B 635 ILE cc_start: 0.7879 (tt) cc_final: 0.6756 (tt) REVERT: C 47 ASP cc_start: 0.8405 (t0) cc_final: 0.8085 (t0) REVERT: C 59 LYS cc_start: 0.7042 (tppt) cc_final: 0.6566 (ttmt) REVERT: C 271 MET cc_start: 0.5475 (tpt) cc_final: 0.5244 (mmm) REVERT: C 288 PHE cc_start: 0.7630 (m-10) cc_final: 0.7212 (m-80) REVERT: C 298 ARG cc_start: 0.8257 (tmm-80) cc_final: 0.7859 (tmm-80) REVERT: D 271 MET cc_start: 0.5844 (tmm) cc_final: 0.5029 (ttt) REVERT: D 342 LEU cc_start: 0.8983 (mp) cc_final: 0.8759 (mt) REVERT: F 575 GLN cc_start: 0.8099 (pp30) cc_final: 0.7470 (mp10) REVERT: F 588 ARG cc_start: 0.8063 (mmt180) cc_final: 0.7798 (mmt180) REVERT: F 591 GLN cc_start: 0.8988 (mt0) cc_final: 0.8756 (mt0) REVERT: F 606 THR cc_start: 0.8394 (m) cc_final: 0.8066 (m) REVERT: F 633 LYS cc_start: 0.7660 (mttt) cc_final: 0.7386 (tppt) REVERT: J 36 TRP cc_start: 0.7515 (m100) cc_final: 0.7257 (m100) REVERT: N 87 TYR cc_start: 0.9033 (m-80) cc_final: 0.8826 (m-80) outliers start: 6 outliers final: 2 residues processed: 407 average time/residue: 0.2793 time to fit residues: 170.9624 Evaluate side-chains 303 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 300 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 72 HIS A 136 ASN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN D 203 GLN E 651 ASN F 540 GLN N 53 HIS ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5696 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17598 Z= 0.271 Angle : 0.790 10.975 23890 Z= 0.387 Chirality : 0.054 0.783 3070 Planarity : 0.004 0.051 2860 Dihedral : 11.890 108.508 4728 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.17 % Allowed : 5.23 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.18), residues: 1944 helix: 0.09 (0.26), residues: 425 sheet: 0.01 (0.21), residues: 530 loop : -0.56 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 610 HIS 0.008 0.001 HIS J 35 PHE 0.030 0.002 PHE C 382 TYR 0.031 0.002 TYR F 643 ARG 0.011 0.001 ARG E 588 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 372 time to evaluate : 1.838 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: A 108 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8417 (mp) REVERT: A 190 GLU cc_start: 0.6762 (pm20) cc_final: 0.6257 (pm20) REVERT: A 216 HIS cc_start: 0.7749 (m-70) cc_final: 0.7487 (m-70) REVERT: A 384 TYR cc_start: 0.7287 (m-80) cc_final: 0.6932 (m-80) REVERT: A 483 LEU cc_start: 0.8958 (mp) cc_final: 0.8223 (mp) REVERT: C 47 ASP cc_start: 0.8543 (t0) cc_final: 0.8205 (t0) REVERT: C 59 LYS cc_start: 0.6957 (tppt) cc_final: 0.6294 (ttmt) REVERT: C 271 MET cc_start: 0.5580 (tpt) cc_final: 0.5337 (tpt) REVERT: C 298 ARG cc_start: 0.8321 (tmm-80) cc_final: 0.7943 (tmm-80) REVERT: C 490 LYS cc_start: 0.8213 (tptp) cc_final: 0.7562 (tptp) REVERT: D 244 THR cc_start: 0.8251 (t) cc_final: 0.7973 (t) REVERT: D 342 LEU cc_start: 0.9238 (mp) cc_final: 0.9025 (mt) REVERT: D 361 PHE cc_start: 0.4835 (m-80) cc_final: 0.4566 (m-80) REVERT: F 575 GLN cc_start: 0.8275 (pp30) cc_final: 0.7508 (mp10) REVERT: F 588 ARG cc_start: 0.8260 (mmt180) cc_final: 0.7892 (mmt180) REVERT: F 601 LYS cc_start: 0.7744 (mppt) cc_final: 0.7141 (pttt) REVERT: F 606 THR cc_start: 0.8699 (m) cc_final: 0.8397 (m) REVERT: F 643 TYR cc_start: 0.8129 (m-80) cc_final: 0.7756 (m-80) REVERT: F 656 ASN cc_start: 0.9100 (t0) cc_final: 0.8897 (t0) REVERT: J 70 THR cc_start: 0.8522 (p) cc_final: 0.8279 (p) outliers start: 3 outliers final: 1 residues processed: 374 average time/residue: 0.2827 time to fit residues: 158.8723 Evaluate side-chains 301 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 299 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 300 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 ASN E 651 ASN F 540 GLN N 53 HIS ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5637 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17598 Z= 0.202 Angle : 0.753 10.916 23890 Z= 0.366 Chirality : 0.053 0.761 3070 Planarity : 0.004 0.063 2860 Dihedral : 11.153 109.766 4728 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.39 (0.19), residues: 1944 helix: 0.24 (0.26), residues: 424 sheet: -0.05 (0.21), residues: 521 loop : -0.50 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 596 HIS 0.007 0.001 HIS N 53 PHE 0.025 0.002 PHE D 288 TYR 0.026 0.002 TYR F 643 ARG 0.009 0.001 ARG E 588 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 1.981 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: A 108 ILE cc_start: 0.8452 (mp) cc_final: 0.8118 (mp) REVERT: A 190 GLU cc_start: 0.6640 (pm20) cc_final: 0.6237 (pm20) REVERT: A 216 HIS cc_start: 0.7733 (m-70) cc_final: 0.7500 (m-70) REVERT: A 384 TYR cc_start: 0.6643 (m-80) cc_final: 0.6271 (m-80) REVERT: A 423 ILE cc_start: 0.7753 (mm) cc_final: 0.7508 (mm) REVERT: A 480 ARG cc_start: 0.7618 (mtp180) cc_final: 0.7138 (ptm160) REVERT: B 635 ILE cc_start: 0.8064 (tt) cc_final: 0.6953 (tt) REVERT: C 47 ASP cc_start: 0.8496 (t0) cc_final: 0.8103 (t0) REVERT: C 59 LYS cc_start: 0.6763 (tppt) cc_final: 0.6135 (ttmt) REVERT: C 271 MET cc_start: 0.5622 (tpt) cc_final: 0.5352 (tpt) REVERT: C 288 PHE cc_start: 0.8047 (m-10) cc_final: 0.7833 (m-10) REVERT: C 298 ARG cc_start: 0.8250 (tmm-80) cc_final: 0.7913 (tmm-80) REVERT: C 490 LYS cc_start: 0.8249 (tptp) cc_final: 0.7665 (tptp) REVERT: D 244 THR cc_start: 0.8335 (t) cc_final: 0.8096 (t) REVERT: D 271 MET cc_start: 0.5856 (tmm) cc_final: 0.5625 (tmm) REVERT: D 361 PHE cc_start: 0.4950 (m-80) cc_final: 0.4672 (m-80) REVERT: E 575 GLN cc_start: 0.9252 (pm20) cc_final: 0.8937 (pm20) REVERT: F 588 ARG cc_start: 0.8041 (mmt180) cc_final: 0.7659 (mmt180) REVERT: F 606 THR cc_start: 0.8735 (m) cc_final: 0.8434 (m) REVERT: F 643 TYR cc_start: 0.8179 (m-80) cc_final: 0.7854 (m-80) REVERT: J 70 THR cc_start: 0.8797 (p) cc_final: 0.8557 (p) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.3188 time to fit residues: 180.5811 Evaluate side-chains 298 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 189 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN F 540 GLN N 53 HIS ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5744 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 17598 Z= 0.274 Angle : 0.807 11.157 23890 Z= 0.394 Chirality : 0.055 0.755 3070 Planarity : 0.005 0.049 2860 Dihedral : 10.520 109.530 4728 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.11 % Allowed : 3.33 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.53 (0.19), residues: 1944 helix: 0.13 (0.26), residues: 419 sheet: -0.12 (0.21), residues: 521 loop : -0.59 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 631 HIS 0.007 0.001 HIS N 53 PHE 0.015 0.002 PHE C 382 TYR 0.025 0.002 TYR F 643 ARG 0.006 0.001 ARG D 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 356 time to evaluate : 1.892 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: A 108 ILE cc_start: 0.8595 (mp) cc_final: 0.8381 (mp) REVERT: A 190 GLU cc_start: 0.6765 (pm20) cc_final: 0.6303 (pm20) REVERT: A 216 HIS cc_start: 0.7803 (m-70) cc_final: 0.7524 (m-70) REVERT: A 340 GLU cc_start: 0.7261 (tp30) cc_final: 0.6743 (pp20) REVERT: A 384 TYR cc_start: 0.7046 (m-80) cc_final: 0.6279 (m-80) REVERT: B 586 TYR cc_start: 0.8588 (t80) cc_final: 0.8366 (t80) REVERT: C 47 ASP cc_start: 0.8640 (t0) cc_final: 0.8297 (t0) REVERT: C 59 LYS cc_start: 0.6769 (tppt) cc_final: 0.6095 (ttmt) REVERT: C 93 PHE cc_start: 0.7122 (m-80) cc_final: 0.6889 (m-80) REVERT: C 271 MET cc_start: 0.6026 (tpt) cc_final: 0.5812 (tpt) REVERT: C 298 ARG cc_start: 0.8263 (tmm-80) cc_final: 0.7931 (tmm-80) REVERT: D 109 ILE cc_start: 0.9115 (pt) cc_final: 0.8583 (pt) REVERT: D 318 TYR cc_start: 0.7254 (m-10) cc_final: 0.6957 (m-80) REVERT: D 361 PHE cc_start: 0.5079 (m-80) cc_final: 0.4771 (m-80) REVERT: D 434 MET cc_start: 0.4161 (ptm) cc_final: 0.2819 (tmm) REVERT: D 452 LEU cc_start: 0.8999 (mt) cc_final: 0.8774 (mt) REVERT: E 635 ILE cc_start: 0.8594 (mm) cc_final: 0.7932 (tp) REVERT: F 575 GLN cc_start: 0.8357 (pp30) cc_final: 0.7008 (mp10) REVERT: F 588 ARG cc_start: 0.8124 (mmt180) cc_final: 0.7736 (mmt180) REVERT: F 601 LYS cc_start: 0.7538 (mppt) cc_final: 0.6947 (pttt) REVERT: F 643 TYR cc_start: 0.8131 (m-80) cc_final: 0.7918 (m-80) REVERT: J 20 VAL cc_start: 0.7410 (p) cc_final: 0.7057 (p) outliers start: 2 outliers final: 1 residues processed: 356 average time/residue: 0.2903 time to fit residues: 154.9445 Evaluate side-chains 277 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 276 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 115 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN D 348 GLN E 651 ASN F 540 GLN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 HIS ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5744 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17598 Z= 0.255 Angle : 0.789 10.363 23890 Z= 0.385 Chirality : 0.054 0.763 3070 Planarity : 0.004 0.059 2860 Dihedral : 10.141 105.683 4728 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.60 (0.19), residues: 1944 helix: 0.06 (0.26), residues: 417 sheet: -0.19 (0.22), residues: 519 loop : -0.61 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 395 HIS 0.007 0.001 HIS N 53 PHE 0.016 0.002 PHE D 382 TYR 0.023 0.002 TYR F 643 ARG 0.007 0.001 ARG E 588 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 1.954 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 108 ILE cc_start: 0.8546 (mp) cc_final: 0.8345 (mp) REVERT: A 225 ILE cc_start: 0.7078 (mt) cc_final: 0.6855 (mt) REVERT: A 384 TYR cc_start: 0.7130 (m-80) cc_final: 0.6479 (m-80) REVERT: B 590 GLN cc_start: 0.9082 (pm20) cc_final: 0.8739 (pm20) REVERT: C 47 ASP cc_start: 0.8708 (t0) cc_final: 0.8361 (t0) REVERT: C 93 PHE cc_start: 0.7728 (m-80) cc_final: 0.7398 (m-80) REVERT: C 99 ASN cc_start: 0.7246 (t0) cc_final: 0.6916 (t0) REVERT: C 100 MET cc_start: 0.6957 (mpp) cc_final: 0.6677 (mpp) REVERT: C 271 MET cc_start: 0.6454 (tpt) cc_final: 0.6194 (tpt) REVERT: C 296 CYS cc_start: 0.5174 (m) cc_final: 0.4935 (m) REVERT: C 298 ARG cc_start: 0.8169 (tmm-80) cc_final: 0.7893 (tmm-80) REVERT: C 308 ARG cc_start: 0.8123 (mmm-85) cc_final: 0.7567 (mmm-85) REVERT: D 111 LEU cc_start: 0.8992 (mt) cc_final: 0.8360 (mt) REVERT: D 341 THR cc_start: 0.9015 (m) cc_final: 0.8712 (p) REVERT: D 342 LEU cc_start: 0.9627 (mm) cc_final: 0.9311 (mt) REVERT: D 452 LEU cc_start: 0.9153 (mt) cc_final: 0.8908 (mt) REVERT: E 575 GLN cc_start: 0.9325 (pm20) cc_final: 0.9024 (pm20) REVERT: E 635 ILE cc_start: 0.8599 (mm) cc_final: 0.8063 (tp) REVERT: F 575 GLN cc_start: 0.8362 (pp30) cc_final: 0.7029 (mp10) REVERT: F 588 ARG cc_start: 0.8183 (mmt180) cc_final: 0.7869 (mmt180) REVERT: F 601 LYS cc_start: 0.7202 (mppt) cc_final: 0.6773 (pttt) REVERT: F 643 TYR cc_start: 0.8113 (m-80) cc_final: 0.7890 (m-80) REVERT: J 20 VAL cc_start: 0.7534 (p) cc_final: 0.7205 (p) REVERT: J 45 LEU cc_start: 0.8521 (tp) cc_final: 0.8066 (tp) REVERT: J 48 MET cc_start: 0.8344 (mtm) cc_final: 0.7984 (mtm) REVERT: J 70 THR cc_start: 0.8951 (p) cc_final: 0.8708 (p) REVERT: J 100 GLU cc_start: 0.7658 (tp30) cc_final: 0.7077 (tm-30) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.3163 time to fit residues: 178.6809 Evaluate side-chains 289 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 148 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN C 374 HIS ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 HIS ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5681 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17598 Z= 0.202 Angle : 0.754 11.778 23890 Z= 0.366 Chirality : 0.052 0.732 3070 Planarity : 0.004 0.055 2860 Dihedral : 9.575 105.264 4728 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.53 (0.19), residues: 1944 helix: 0.14 (0.26), residues: 423 sheet: -0.11 (0.23), residues: 503 loop : -0.60 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 395 HIS 0.007 0.001 HIS J 52A PHE 0.014 0.001 PHE D 382 TYR 0.021 0.001 TYR F 643 ARG 0.008 0.001 ARG E 588 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 1.914 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: A 108 ILE cc_start: 0.8470 (mp) cc_final: 0.8188 (mp) REVERT: A 190 GLU cc_start: 0.6648 (pm20) cc_final: 0.6417 (pm20) REVERT: A 216 HIS cc_start: 0.7774 (m-70) cc_final: 0.7450 (m-70) REVERT: A 384 TYR cc_start: 0.7278 (m-80) cc_final: 0.6544 (m-80) REVERT: C 47 ASP cc_start: 0.8632 (t0) cc_final: 0.8216 (t0) REVERT: C 93 PHE cc_start: 0.7778 (m-80) cc_final: 0.7436 (m-80) REVERT: C 100 MET cc_start: 0.6884 (mpp) cc_final: 0.6376 (mpp) REVERT: C 116 LEU cc_start: 0.8928 (mt) cc_final: 0.8596 (mt) REVERT: C 271 MET cc_start: 0.6186 (tpt) cc_final: 0.5980 (tpt) REVERT: C 298 ARG cc_start: 0.8157 (tmm-80) cc_final: 0.7882 (tmm-80) REVERT: D 342 LEU cc_start: 0.9585 (mm) cc_final: 0.9225 (mt) REVERT: E 575 GLN cc_start: 0.9254 (pm20) cc_final: 0.9015 (mp10) REVERT: E 635 ILE cc_start: 0.8600 (mm) cc_final: 0.8257 (tp) REVERT: F 575 GLN cc_start: 0.8358 (pp30) cc_final: 0.7084 (mp10) REVERT: F 588 ARG cc_start: 0.8190 (mmt180) cc_final: 0.7823 (mmt180) REVERT: F 601 LYS cc_start: 0.7381 (mppt) cc_final: 0.6873 (pttt) REVERT: F 643 TYR cc_start: 0.8066 (m-80) cc_final: 0.7705 (m-80) REVERT: J 20 VAL cc_start: 0.7633 (p) cc_final: 0.7129 (p) REVERT: J 48 MET cc_start: 0.8189 (mtm) cc_final: 0.7907 (mtm) REVERT: J 70 THR cc_start: 0.8951 (p) cc_final: 0.8667 (p) REVERT: J 100 GLU cc_start: 0.7493 (tp30) cc_final: 0.7081 (tp30) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.2906 time to fit residues: 163.3696 Evaluate side-chains 296 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 138 optimal weight: 0.0670 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 0.0770 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 overall best weight: 0.8078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 HIS ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5679 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17598 Z= 0.201 Angle : 0.775 12.354 23890 Z= 0.381 Chirality : 0.054 0.786 3070 Planarity : 0.004 0.052 2860 Dihedral : 9.318 104.753 4728 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.54 (0.19), residues: 1944 helix: 0.21 (0.27), residues: 422 sheet: -0.11 (0.22), residues: 498 loop : -0.66 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 479 HIS 0.006 0.001 HIS N 53 PHE 0.025 0.002 PHE A 382 TYR 0.021 0.001 TYR F 643 ARG 0.008 0.001 ARG N 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 1.969 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: A 108 ILE cc_start: 0.8307 (mp) cc_final: 0.8047 (mp) REVERT: A 216 HIS cc_start: 0.7750 (m-70) cc_final: 0.7441 (m-70) REVERT: A 384 TYR cc_start: 0.7272 (m-80) cc_final: 0.6399 (m-80) REVERT: A 480 ARG cc_start: 0.7596 (mtp180) cc_final: 0.7295 (ptm160) REVERT: B 586 TYR cc_start: 0.8568 (t80) cc_final: 0.8303 (t80) REVERT: C 47 ASP cc_start: 0.8533 (t0) cc_final: 0.8137 (t0) REVERT: C 59 LYS cc_start: 0.6400 (tptt) cc_final: 0.6088 (tppt) REVERT: C 93 PHE cc_start: 0.7765 (m-80) cc_final: 0.7505 (m-80) REVERT: C 271 MET cc_start: 0.6143 (tpt) cc_final: 0.5904 (tpt) REVERT: C 298 ARG cc_start: 0.8131 (tmm-80) cc_final: 0.7892 (tmm-80) REVERT: C 434 MET cc_start: 0.6379 (mtm) cc_final: 0.6146 (mtp) REVERT: D 342 LEU cc_start: 0.9575 (mm) cc_final: 0.9202 (mt) REVERT: D 434 MET cc_start: 0.4146 (ptm) cc_final: 0.3375 (tmm) REVERT: E 575 GLN cc_start: 0.9240 (pm20) cc_final: 0.9011 (pm20) REVERT: E 584 GLU cc_start: 0.8998 (pm20) cc_final: 0.8675 (pm20) REVERT: E 593 LEU cc_start: 0.8627 (mt) cc_final: 0.8404 (mt) REVERT: E 635 ILE cc_start: 0.8608 (mm) cc_final: 0.8281 (tp) REVERT: F 575 GLN cc_start: 0.8371 (pp30) cc_final: 0.7099 (mp10) REVERT: F 601 LYS cc_start: 0.7135 (mppt) cc_final: 0.6735 (pttt) REVERT: F 643 TYR cc_start: 0.8045 (m-80) cc_final: 0.7646 (m-80) REVERT: J 20 VAL cc_start: 0.7721 (p) cc_final: 0.7196 (p) REVERT: J 48 MET cc_start: 0.8279 (mtm) cc_final: 0.8000 (mtm) REVERT: J 70 THR cc_start: 0.8920 (p) cc_final: 0.8607 (p) REVERT: J 100 GLU cc_start: 0.7373 (tp30) cc_final: 0.6846 (tp30) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.2871 time to fit residues: 158.4532 Evaluate side-chains 288 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 8.9990 chunk 186 optimal weight: 0.0770 chunk 113 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 195 optimal weight: 0.0870 chunk 179 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 120 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5673 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 17598 Z= 0.208 Angle : 0.779 17.978 23890 Z= 0.382 Chirality : 0.053 0.703 3070 Planarity : 0.004 0.054 2860 Dihedral : 9.207 116.946 4728 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.54 (0.19), residues: 1944 helix: 0.27 (0.27), residues: 422 sheet: -0.08 (0.22), residues: 495 loop : -0.70 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 479 HIS 0.005 0.001 HIS N 53 PHE 0.014 0.001 PHE D 382 TYR 0.021 0.001 TYR F 643 ARG 0.016 0.001 ARG E 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 1.667 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: A 107 ASP cc_start: 0.8176 (m-30) cc_final: 0.7775 (m-30) REVERT: A 108 ILE cc_start: 0.8222 (mp) cc_final: 0.7961 (mp) REVERT: A 216 HIS cc_start: 0.7685 (m-70) cc_final: 0.7329 (m-70) REVERT: A 384 TYR cc_start: 0.7268 (m-80) cc_final: 0.6328 (m-80) REVERT: A 480 ARG cc_start: 0.7625 (mtp180) cc_final: 0.7301 (ptm160) REVERT: B 545 LEU cc_start: 0.6274 (pp) cc_final: 0.5803 (pp) REVERT: B 586 TYR cc_start: 0.8531 (t80) cc_final: 0.8252 (t80) REVERT: C 47 ASP cc_start: 0.8574 (t0) cc_final: 0.8106 (t0) REVERT: C 59 LYS cc_start: 0.6567 (tptt) cc_final: 0.6274 (tppt) REVERT: C 93 PHE cc_start: 0.7816 (m-80) cc_final: 0.7437 (m-80) REVERT: C 271 MET cc_start: 0.6153 (tpt) cc_final: 0.5814 (tpt) REVERT: C 298 ARG cc_start: 0.8197 (tmm-80) cc_final: 0.7891 (tmm-80) REVERT: C 434 MET cc_start: 0.6399 (mtm) cc_final: 0.6158 (mtp) REVERT: D 302 ASN cc_start: 0.8603 (m-40) cc_final: 0.7986 (p0) REVERT: D 342 LEU cc_start: 0.9510 (mm) cc_final: 0.9076 (mt) REVERT: D 434 MET cc_start: 0.4098 (ptm) cc_final: 0.3386 (tmm) REVERT: E 536 THR cc_start: 0.8931 (p) cc_final: 0.8700 (p) REVERT: E 540 GLN cc_start: 0.6992 (mm-40) cc_final: 0.6478 (mm-40) REVERT: E 635 ILE cc_start: 0.8475 (mm) cc_final: 0.8158 (tp) REVERT: E 642 ILE cc_start: 0.8281 (mm) cc_final: 0.8070 (mm) REVERT: F 601 LYS cc_start: 0.7188 (mppt) cc_final: 0.6776 (pttt) REVERT: F 643 TYR cc_start: 0.8016 (m-80) cc_final: 0.7618 (m-80) REVERT: J 20 VAL cc_start: 0.7840 (p) cc_final: 0.7176 (p) REVERT: J 37 VAL cc_start: 0.8515 (t) cc_final: 0.8305 (t) REVERT: J 48 MET cc_start: 0.8310 (mtm) cc_final: 0.7970 (mtm) REVERT: J 70 THR cc_start: 0.8923 (p) cc_final: 0.8662 (p) REVERT: J 100 GLU cc_start: 0.7178 (tp30) cc_final: 0.6811 (tp30) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.2754 time to fit residues: 153.7970 Evaluate side-chains 290 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 143 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 159 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 ASN ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 GLN N 53 HIS ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.129597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.097272 restraints weight = 57467.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.100299 restraints weight = 42028.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.102507 restraints weight = 31789.254| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 17598 Z= 0.409 Angle : 0.973 16.492 23890 Z= 0.478 Chirality : 0.062 1.030 3070 Planarity : 0.006 0.076 2860 Dihedral : 9.946 112.296 4728 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 26.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.21 (0.18), residues: 1944 helix: -0.78 (0.24), residues: 420 sheet: -0.44 (0.22), residues: 507 loop : -0.92 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.004 TRP E 571 HIS 0.013 0.002 HIS D 216 PHE 0.023 0.003 PHE C 93 TYR 0.021 0.003 TYR A 484 ARG 0.015 0.001 ARG C 308 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3717.26 seconds wall clock time: 67 minutes 39.45 seconds (4059.45 seconds total)