Starting phenix.real_space_refine on Sun Jun 15 04:01:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bnl_44729/06_2025/9bnl_44729.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bnl_44729/06_2025/9bnl_44729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bnl_44729/06_2025/9bnl_44729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bnl_44729/06_2025/9bnl_44729.map" model { file = "/net/cci-nas-00/data/ceres_data/9bnl_44729/06_2025/9bnl_44729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bnl_44729/06_2025/9bnl_44729.cif" } resolution = 3.6 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= 0.002 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 103 5.16 5 C 10479 2.51 5 N 2734 2.21 5 O 3433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16749 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3472 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "B" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 970 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "C" Number of atoms: 3452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3452 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Chain: "E" Number of atoms: 3452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3452 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Chain: "F" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 970 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "G" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 970 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1031 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: 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: "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: 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: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 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: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 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: "A" 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: "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: 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" 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 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASN L 92 " occ=0.98 ... (6 atoms not shown) pdb=" ND2 ASN L 92 " occ=0.98 Time building chain proxies: 11.10, per 1000 atoms: 0.66 Number of scatterers: 16749 At special positions: 0 Unit cell: (124.5, 126.16, 154.38, 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 103 16.00 O 3433 8.00 N 2734 7.00 C 10479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=1.98 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 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 B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.00 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.01 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=1.79 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN u 4 " - " MAN u 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA h 3 " - " MAN h 4 " " BMA u 3 " - " MAN u 4 " ALPHA1-6 " BMA h 3 " - " MAN h 5 " " BMA u 3 " - " MAN u 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " 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 P 2 " - " BMA P 3 " " 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 U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " 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 g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " 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 u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 601 " - " ASN A 386 " " NAG A 602 " - " ASN A 339 " " NAG A 603 " - " ASN A 88 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 625 " " NAG C 601 " - " ASN C 339 " " NAG C 602 " - " ASN C 386 " " NAG C 603 " - " ASN C 448 " " NAG C 604 " - " ASN C 88 " " NAG C 605 " - " ASN C 133 " " NAG D 1 " - " ASN A 156 " " NAG E 601 " - " ASN E 339 " " NAG E 602 " - " ASN E 386 " " NAG E 603 " - " ASN E 448 " " NAG E 604 " - " ASN E 465 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 625 " " NAG F 703 " - " ASN F 637 " " NAG G 701 " - " ASN G 637 " " NAG G 702 " - " ASN G 625 " " NAG G 703 " - " ASN G 611 " " NAG I 1 " - " ASN A 241 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 276 " " NAG M 1 " - " ASN A 465 " " NAG N 1 " - " ASN A 392 " " NAG O 1 " - " ASN A 363 " " NAG P 1 " - " ASN A 332 " " NAG Q 1 " - " ASN A 301 " " NAG R 1 " - " ASN A 133 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN A 197 " " NAG U 1 " - " ASN A 160 " " NAG V 1 " - " ASN A 448 " " NAG W 1 " - " ASN B 611 " " NAG X 1 " - " ASN C 156 " " NAG Y 1 " - " ASN C 241 " " NAG Z 1 " - " ASN C 234 " " NAG a 1 " - " ASN C 276 " " NAG b 1 " - " ASN C 465 " " NAG c 1 " - " ASN C 363 " " NAG d 1 " - " ASN C 332 " " NAG e 1 " - " ASN C 301 " " NAG f 1 " - " ASN C 262 " " NAG g 1 " - " ASN C 197 " " NAG h 1 " - " ASN C 160 " " NAG i 1 " - " ASN C 392 " " NAG j 1 " - " ASN E 156 " " NAG k 1 " - " ASN E 88 " " NAG l 1 " - " ASN E 241 " " NAG m 1 " - " ASN E 276 " " NAG n 1 " - " ASN E 392 " " NAG o 1 " - " ASN E 363 " " NAG p 1 " - " ASN E 332 " " NAG q 1 " - " ASN E 301 " " NAG r 1 " - " ASN E 133 " " NAG s 1 " - " ASN E 262 " " NAG t 1 " - " ASN E 197 " " NAG u 1 " - " ASN E 160 " " NAG v 1 " - " ASN E 234 " Time building additional restraints: 5.50 Conformation dependent library (CDL) restraints added in 2.0 seconds 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3570 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 34 sheets defined 23.9% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.553A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.679A pdb=" N THR A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.603A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.842A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.234A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.864A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 removed outlier: 4.044A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 661 removed outlier: 4.667A pdb=" N GLN B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LEU B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.649A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL C 127 " --> pdb=" O PRO C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 386 through 390 removed outlier: 4.060A pdb=" N GLY C 389 " --> pdb=" O ASN C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.873A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.954A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 486 removed outlier: 4.377A pdb=" N LYS C 485 " --> pdb=" O GLU C 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 127 removed outlier: 3.772A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL E 127 " --> pdb=" O PRO E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.814A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.615A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.461A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.570A pdb=" N ASP F 589 " --> pdb=" O HIS F 585 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU F 593 " --> pdb=" O ASP F 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 635 through 661 removed outlier: 4.396A pdb=" N GLN F 640 " --> pdb=" O ASN F 636 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS F 658 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU F 659 " --> pdb=" O LYS F 655 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU F 660 " --> pdb=" O ASN F 656 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU F 661 " --> pdb=" O GLU F 657 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 537 through 544 removed outlier: 3.544A pdb=" N ALA G 541 " --> pdb=" O LEU G 537 " (cutoff:3.500A) Processing helix chain 'G' and resid 569 through 596 removed outlier: 3.579A pdb=" N LEU G 592 " --> pdb=" O ARG G 588 " (cutoff:3.500A) Processing helix chain 'G' and resid 618 through 625 Processing helix chain 'G' and resid 627 through 635 removed outlier: 3.591A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE G 635 " --> pdb=" O TRP G 631 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 661 removed outlier: 3.599A pdb=" N ARG G 644 " --> pdb=" O GLN G 640 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.646A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.178A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.710A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.649A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.475A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.538A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N LYS A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.544A pdb=" N ILE A 294 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 9.973A pdb=" N GLU A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.967A pdb=" N VAL A 292 " --> pdb=" O GLU A 446 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ASN A 448 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 10.092A pdb=" N GLN A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR A 293 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR A 334 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS A 330 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.795A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.092A pdb=" N GLN A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ASN A 448 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 10.967A pdb=" N VAL A 292 " --> pdb=" O GLU A 446 " (cutoff:3.500A) removed outlier: 9.973A pdb=" N GLU A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.544A pdb=" N ILE A 294 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N LYS A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.694A 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 309 Processing sheet with id=AA9, first strand: chain 'C' and resid 495 through 499 Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.686A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.757A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB5, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.381A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 260 through 261 removed outlier: 10.389A pdb=" N LYS C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.674A pdb=" N ILE C 294 " --> pdb=" O LYS C 444 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N GLU C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.861A pdb=" N VAL C 292 " --> pdb=" O GLU C 446 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N ASN C 448 " --> pdb=" O GLN C 290 " (cutoff:3.500A) removed outlier: 9.827A pdb=" N GLN C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 298 current: chain 'C' and resid 358 through 361 removed outlier: 3.718A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.365A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 9.827A pdb=" N GLN C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N ASN C 448 " --> pdb=" O GLN C 290 " (cutoff:3.500A) removed outlier: 10.861A pdb=" N VAL C 292 " --> pdb=" O GLU C 446 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N GLU C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.674A pdb=" N ILE C 294 " --> pdb=" O LYS C 444 " (cutoff:3.500A) removed outlier: 10.389A pdb=" N LYS C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 443 through 456 current: chain 'C' and resid 413 through 418 Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 312 removed outlier: 6.687A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.559A pdb=" N CYS C 385 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.544A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.517A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AC6, first strand: chain 'E' and resid 154 through 162 Processing sheet with id=AC7, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.363A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.613A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N LYS E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.544A pdb=" N ILE E 294 " --> pdb=" O LYS E 444 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N GLU E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.805A pdb=" N VAL E 292 " --> pdb=" O GLU E 446 " (cutoff:3.500A) removed outlier: 9.429A pdb=" N ASN E 448 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 10.012A pdb=" N GLN E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N THR E 293 " --> pdb=" O THR E 334 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR E 334 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.660A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.012A pdb=" N GLN E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.429A pdb=" N ASN E 448 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 10.805A pdb=" N VAL E 292 " --> pdb=" O GLU E 446 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N GLU E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.544A pdb=" N ILE E 294 " --> pdb=" O LYS E 444 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N LYS E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU E 466 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AD4, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.058A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.818A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU L 47 " --> pdb=" O TRP L 35 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.094A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1551 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: 5.34 Time building geometry restraints manager: 6.31 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: 5016 1.34 - 1.47: 4442 1.47 - 1.59: 7479 1.59 - 1.72: 1 1.72 - 1.84: 134 Bond restraints: 17072 Sorted by residual: bond pdb=" N GLY A 237 " pdb=" CA GLY A 237 " ideal model delta sigma weight residual 1.447 1.476 -0.029 9.20e-03 1.18e+04 9.91e+00 bond pdb=" N ILE C 359 " pdb=" CA ILE C 359 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.20e-02 6.94e+03 8.47e+00 bond pdb=" N ILE A 184 " pdb=" CA ILE A 184 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.19e-02 7.06e+03 7.99e+00 bond pdb=" C MET H 82C" pdb=" N ASP H 83 " ideal model delta sigma weight residual 1.331 1.375 -0.044 1.59e-02 3.96e+03 7.72e+00 bond pdb=" N LEU A 52 " pdb=" CA LEU A 52 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.70e+00 ... (remaining 17067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 22741 2.74 - 5.48: 419 5.48 - 8.21: 19 8.21 - 10.95: 1 10.95 - 13.69: 2 Bond angle restraints: 23182 Sorted by residual: angle pdb=" C CYS C 54 " pdb=" CA CYS C 54 " pdb=" CB CYS C 54 " ideal model delta sigma weight residual 109.76 98.68 11.08 1.99e+00 2.53e-01 3.10e+01 angle pdb=" CB MET F 530 " pdb=" CG MET F 530 " pdb=" SD MET F 530 " ideal model delta sigma weight residual 112.70 126.39 -13.69 3.00e+00 1.11e-01 2.08e+01 angle pdb=" N ASN E 302 " pdb=" CA ASN E 302 " pdb=" C ASN E 302 " ideal model delta sigma weight residual 110.91 115.98 -5.07 1.17e+00 7.31e-01 1.88e+01 angle pdb=" N CYS A 378 " pdb=" CA CYS A 378 " pdb=" C CYS A 378 " ideal model delta sigma weight residual 109.15 115.25 -6.10 1.44e+00 4.82e-01 1.79e+01 angle pdb=" N ASN A 234 " pdb=" CA ASN A 234 " pdb=" C ASN A 234 " ideal model delta sigma weight residual 113.20 108.16 5.04 1.21e+00 6.83e-01 1.73e+01 ... (remaining 23177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.04: 10944 21.04 - 42.07: 625 42.07 - 63.11: 166 63.11 - 84.14: 39 84.14 - 105.18: 9 Dihedral angle restraints: 11783 sinusoidal: 6262 harmonic: 5521 Sorted by residual: dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -159.70 73.70 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.41 -57.41 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 143.52 -50.52 1 1.00e+01 1.00e-02 3.50e+01 ... (remaining 11780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2526 0.065 - 0.131: 366 0.131 - 0.196: 57 0.196 - 0.261: 11 0.261 - 0.327: 2 Chirality restraints: 2962 Sorted by residual: chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.35e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.37e+01 chirality pdb=" CA CYS C 54 " pdb=" N CYS C 54 " pdb=" C CYS C 54 " pdb=" CB CYS C 54 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 2959 not shown) Planarity restraints: 2831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " 0.091 2.00e-02 2.50e+03 7.45e-02 6.93e+01 pdb=" C7 NAG J 1 " -0.022 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " 0.068 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " -0.119 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 192 " 0.216 9.50e-02 1.11e+02 9.67e-02 5.80e+00 pdb=" NE ARG A 192 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 192 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 192 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 192 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 211 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO C 212 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 212 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 212 " 0.029 5.00e-02 4.00e+02 ... (remaining 2828 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 994 2.73 - 3.27: 17100 3.27 - 3.82: 26207 3.82 - 4.36: 31302 4.36 - 4.90: 53853 Nonbonded interactions: 129456 Sorted by model distance: nonbonded pdb=" O LEU E 369 " pdb=" OG1 THR E 373 " model vdw 2.191 3.040 nonbonded pdb=" O ILE F 535 " pdb=" ND2 ASN G 651 " model vdw 2.192 3.120 nonbonded pdb=" OG SER A 199 " pdb=" O GLY A 431 " model vdw 2.242 3.040 nonbonded pdb=" CD2 HIS A 85 " pdb=" OD1 ASP A 87 " model vdw 2.312 3.260 nonbonded pdb=" O3 NAG d 2 " pdb=" O5 BMA d 3 " model vdw 2.317 3.040 ... (remaining 129451 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 185 or resid 188 through 505 or resid 601 throu \ gh 603)) selection = (chain 'C' and (resid 33 through 135 or resid 152 through 505 or resid 601 throu \ gh 603)) selection = (chain 'E' and (resid 33 through 135 or resid 152 through 505 or resid 601 throu \ gh 603)) } ncs_group { reference = chain 'B' selection = (chain 'F' and (resid 520 through 661 or resid 701 through 702)) selection = (chain 'G' and (resid 520 through 661 or resid 701 through 702)) } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'v' } ncs_group { reference = chain 'J' selection = chain 'P' selection = chain 'S' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'f' selection = chain 'j' selection = chain 'l' selection = chain 'p' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.98 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 40.900 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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 0.242 17226 Z= 0.261 Angle : 0.987 17.959 23610 Z= 0.507 Chirality : 0.050 0.327 2962 Planarity : 0.005 0.097 2771 Dihedral : 13.613 105.178 8111 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.19), residues: 1864 helix: 0.25 (0.26), residues: 401 sheet: -0.67 (0.22), residues: 496 loop : -1.47 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 628 HIS 0.008 0.001 HIS E 249 PHE 0.029 0.002 PHE L 83 TYR 0.008 0.001 TYR E 217 ARG 0.005 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 60) link_NAG-ASN : angle 2.26916 ( 180) link_ALPHA1-6 : bond 0.01979 ( 2) link_ALPHA1-6 : angle 3.51430 ( 6) link_BETA1-4 : bond 0.01505 ( 54) link_BETA1-4 : angle 4.55657 ( 162) link_ALPHA1-2 : bond 0.00929 ( 1) link_ALPHA1-2 : angle 3.66988 ( 3) link_ALPHA1-3 : bond 0.01413 ( 3) link_ALPHA1-3 : angle 3.91508 ( 9) hydrogen bonds : bond 0.22800 ( 556) hydrogen bonds : angle 8.31119 ( 1551) SS BOND : bond 0.04301 ( 34) SS BOND : angle 3.54481 ( 68) covalent geometry : bond 0.00438 (17072) covalent geometry : angle 0.87106 (23182) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 647 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8405 (mt-10) REVERT: B 654 GLU cc_start: 0.9442 (mm-30) cc_final: 0.8372 (mp0) REVERT: C 95 MET cc_start: 0.7649 (ptp) cc_final: 0.7332 (ptp) REVERT: C 195 ASN cc_start: 0.8057 (m110) cc_final: 0.7814 (m110) REVERT: C 434 MET cc_start: 0.8799 (tpp) cc_final: 0.8067 (tpp) REVERT: F 642 ILE cc_start: 0.9630 (mt) cc_final: 0.9416 (mt) REVERT: H 36 TRP cc_start: 0.8005 (m100) cc_final: 0.7356 (m100) REVERT: H 82 ASN cc_start: 0.9285 (m-40) cc_final: 0.8685 (t0) REVERT: H 82 MET cc_start: 0.8374 (mmm) cc_final: 0.7750 (mmm) REVERT: H 100 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8094 (mm-30) REVERT: H 100 MET cc_start: 0.8340 (tpp) cc_final: 0.8067 (tpp) REVERT: H 105 GLN cc_start: 0.8750 (pt0) cc_final: 0.8484 (pt0) REVERT: H 108 ARG cc_start: 0.8515 (mmt90) cc_final: 0.8026 (tpt-90) REVERT: L 17 ASP cc_start: 0.9106 (t0) cc_final: 0.8815 (p0) REVERT: L 87 TYR cc_start: 0.8238 (m-80) cc_final: 0.7802 (m-10) REVERT: L 105 ASP cc_start: 0.8363 (t0) cc_final: 0.7994 (p0) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.3005 time to fit residues: 53.7268 Evaluate side-chains 75 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.1980 chunk 142 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 170 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN A 425 ASN E 246 GLN ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN G 650 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.045828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.036120 restraints weight = 107644.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.037407 restraints weight = 55367.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.038251 restraints weight = 37692.103| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17226 Z= 0.168 Angle : 0.741 16.872 23610 Z= 0.340 Chirality : 0.047 0.408 2962 Planarity : 0.004 0.043 2771 Dihedral : 9.148 69.726 4516 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.30 % Allowed : 9.22 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.19), residues: 1864 helix: 1.04 (0.26), residues: 405 sheet: -0.60 (0.22), residues: 520 loop : -1.24 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 631 HIS 0.005 0.001 HIS E 249 PHE 0.012 0.002 PHE C 353 TYR 0.014 0.001 TYR C 352 ARG 0.005 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 60) link_NAG-ASN : angle 2.08548 ( 180) link_ALPHA1-6 : bond 0.00907 ( 2) link_ALPHA1-6 : angle 1.39262 ( 6) link_BETA1-4 : bond 0.00981 ( 54) link_BETA1-4 : angle 3.20947 ( 162) link_ALPHA1-2 : bond 0.00526 ( 1) link_ALPHA1-2 : angle 2.85479 ( 3) link_ALPHA1-3 : bond 0.01101 ( 3) link_ALPHA1-3 : angle 2.51385 ( 9) hydrogen bonds : bond 0.05272 ( 556) hydrogen bonds : angle 5.72152 ( 1551) SS BOND : bond 0.00337 ( 34) SS BOND : angle 1.06184 ( 68) covalent geometry : bond 0.00363 (17072) covalent geometry : angle 0.66796 (23182) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 THR cc_start: 0.9332 (OUTLIER) cc_final: 0.8879 (p) REVERT: B 647 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8202 (mt-10) REVERT: C 95 MET cc_start: 0.8122 (ptp) cc_final: 0.7854 (ptp) REVERT: C 161 MET cc_start: 0.8590 (tpt) cc_final: 0.8291 (tpt) REVERT: C 195 ASN cc_start: 0.8226 (m110) cc_final: 0.8001 (m110) REVERT: C 434 MET cc_start: 0.8748 (tpp) cc_final: 0.8342 (tpp) REVERT: C 475 MET cc_start: 0.9194 (tpp) cc_final: 0.8993 (tpt) REVERT: E 492 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8554 (tt0) REVERT: F 652 GLN cc_start: 0.8994 (tp40) cc_final: 0.8715 (tp-100) REVERT: G 590 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8777 (tm-30) REVERT: G 654 GLU cc_start: 0.8991 (tp30) cc_final: 0.8676 (tp30) REVERT: H 36 TRP cc_start: 0.8303 (m100) cc_final: 0.7686 (m100) REVERT: H 46 GLU cc_start: 0.8765 (tt0) cc_final: 0.8372 (tt0) REVERT: H 82 MET cc_start: 0.8548 (mmm) cc_final: 0.8078 (mmm) REVERT: H 100 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8089 (mm-30) REVERT: H 105 GLN cc_start: 0.8708 (pt0) cc_final: 0.8467 (pt0) REVERT: H 108 ARG cc_start: 0.8615 (mmt90) cc_final: 0.8091 (tpt-90) REVERT: L 4 MET cc_start: 0.8845 (tpp) cc_final: 0.8562 (tpp) REVERT: L 105 ASP cc_start: 0.8554 (t0) cc_final: 0.8172 (p0) outliers start: 22 outliers final: 8 residues processed: 103 average time/residue: 0.2571 time to fit residues: 43.3970 Evaluate side-chains 83 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 492 GLU Chi-restraints excluded: chain H residue 78 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 0 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN E 85 HIS E 377 ASN H 105 GLN L 3 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.043887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.033980 restraints weight = 108499.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.035179 restraints weight = 56068.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.035981 restraints weight = 38826.780| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 17226 Z= 0.261 Angle : 0.759 16.792 23610 Z= 0.348 Chirality : 0.047 0.396 2962 Planarity : 0.004 0.053 2771 Dihedral : 9.061 69.416 4516 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.30 % Allowed : 10.40 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.19), residues: 1864 helix: 1.22 (0.26), residues: 399 sheet: -0.54 (0.21), residues: 533 loop : -1.21 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 479 HIS 0.005 0.002 HIS E 330 PHE 0.014 0.002 PHE A 376 TYR 0.011 0.001 TYR E 177 ARG 0.003 0.001 ARG E 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 60) link_NAG-ASN : angle 2.19234 ( 180) link_ALPHA1-6 : bond 0.00677 ( 2) link_ALPHA1-6 : angle 1.37766 ( 6) link_BETA1-4 : bond 0.00900 ( 54) link_BETA1-4 : angle 2.99209 ( 162) link_ALPHA1-2 : bond 0.00972 ( 1) link_ALPHA1-2 : angle 3.38661 ( 3) link_ALPHA1-3 : bond 0.00981 ( 3) link_ALPHA1-3 : angle 2.68189 ( 9) hydrogen bonds : bond 0.04682 ( 556) hydrogen bonds : angle 5.27800 ( 1551) SS BOND : bond 0.00427 ( 34) SS BOND : angle 1.12988 ( 68) covalent geometry : bond 0.00573 (17072) covalent geometry : angle 0.69176 (23182) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9466 (ttm) cc_final: 0.9096 (ttm) REVERT: A 257 THR cc_start: 0.9440 (OUTLIER) cc_final: 0.9092 (p) REVERT: B 530 MET cc_start: 0.8910 (mmm) cc_final: 0.8688 (tpp) REVERT: B 647 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8248 (mt-10) REVERT: B 657 GLU cc_start: 0.9158 (tt0) cc_final: 0.8758 (tm-30) REVERT: C 434 MET cc_start: 0.8696 (tpp) cc_final: 0.8494 (tpp) REVERT: F 648 GLU cc_start: 0.9237 (pt0) cc_final: 0.8924 (pp20) REVERT: G 590 GLN cc_start: 0.9112 (tm-30) cc_final: 0.8630 (tm-30) REVERT: H 34 MET cc_start: 0.9186 (tpp) cc_final: 0.8732 (mmm) REVERT: H 82 MET cc_start: 0.8968 (mmm) cc_final: 0.8351 (mmm) REVERT: H 100 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8002 (tp30) REVERT: H 108 ARG cc_start: 0.8655 (mmt90) cc_final: 0.8209 (tpt-90) REVERT: L 3 GLN cc_start: 0.9436 (OUTLIER) cc_final: 0.9194 (tp40) REVERT: L 105 ASP cc_start: 0.8635 (t0) cc_final: 0.8234 (p0) outliers start: 22 outliers final: 9 residues processed: 90 average time/residue: 0.2818 time to fit residues: 41.8639 Evaluate side-chains 73 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain F residue 585 HIS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain L residue 3 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 29 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 chunk 177 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.044361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.034554 restraints weight = 105399.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.035808 restraints weight = 54001.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.036637 restraints weight = 36827.123| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17226 Z= 0.162 Angle : 0.666 16.869 23610 Z= 0.303 Chirality : 0.045 0.406 2962 Planarity : 0.003 0.038 2771 Dihedral : 8.773 66.176 4516 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.95 % Allowed : 11.35 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.19), residues: 1864 helix: 1.37 (0.26), residues: 402 sheet: -0.43 (0.22), residues: 523 loop : -1.14 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 53 HIS 0.005 0.001 HIS E 249 PHE 0.011 0.001 PHE L 98 TYR 0.007 0.001 TYR C 39 ARG 0.002 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 60) link_NAG-ASN : angle 1.97129 ( 180) link_ALPHA1-6 : bond 0.00816 ( 2) link_ALPHA1-6 : angle 1.33288 ( 6) link_BETA1-4 : bond 0.00920 ( 54) link_BETA1-4 : angle 2.82894 ( 162) link_ALPHA1-2 : bond 0.00638 ( 1) link_ALPHA1-2 : angle 2.83060 ( 3) link_ALPHA1-3 : bond 0.00912 ( 3) link_ALPHA1-3 : angle 2.61032 ( 9) hydrogen bonds : bond 0.04027 ( 556) hydrogen bonds : angle 5.01097 ( 1551) SS BOND : bond 0.00306 ( 34) SS BOND : angle 0.84835 ( 68) covalent geometry : bond 0.00355 (17072) covalent geometry : angle 0.59923 (23182) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9469 (ttm) cc_final: 0.9125 (ttm) REVERT: A 257 THR cc_start: 0.9399 (OUTLIER) cc_final: 0.9061 (p) REVERT: B 647 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8339 (mt-10) REVERT: B 657 GLU cc_start: 0.9181 (tt0) cc_final: 0.8742 (tm-30) REVERT: E 475 MET cc_start: 0.9404 (tpt) cc_final: 0.9185 (tpp) REVERT: F 648 GLU cc_start: 0.9233 (pt0) cc_final: 0.8935 (pp20) REVERT: G 657 GLU cc_start: 0.9057 (tt0) cc_final: 0.8776 (pp20) REVERT: H 34 MET cc_start: 0.9211 (tpp) cc_final: 0.8781 (mmm) REVERT: H 46 GLU cc_start: 0.8926 (tt0) cc_final: 0.8518 (tt0) REVERT: H 100 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7982 (tp30) REVERT: H 108 ARG cc_start: 0.8682 (mmt90) cc_final: 0.8156 (tpt-90) REVERT: L 3 GLN cc_start: 0.9402 (OUTLIER) cc_final: 0.9165 (tp40) REVERT: L 105 ASP cc_start: 0.8688 (t0) cc_final: 0.8310 (p0) outliers start: 16 outliers final: 7 residues processed: 81 average time/residue: 0.2500 time to fit residues: 34.0047 Evaluate side-chains 71 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain F residue 585 HIS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain L residue 3 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 146 optimal weight: 8.9990 chunk 11 optimal weight: 0.2980 chunk 68 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 180 optimal weight: 0.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN L 3 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.044107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.034239 restraints weight = 107621.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.035511 restraints weight = 55135.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.036344 restraints weight = 37383.931| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17226 Z= 0.180 Angle : 0.663 16.946 23610 Z= 0.302 Chirality : 0.045 0.405 2962 Planarity : 0.003 0.037 2771 Dihedral : 8.728 64.614 4516 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.48 % Allowed : 11.58 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.19), residues: 1864 helix: 1.39 (0.26), residues: 402 sheet: -0.41 (0.22), residues: 528 loop : -1.12 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 53 HIS 0.004 0.001 HIS E 249 PHE 0.009 0.001 PHE L 83 TYR 0.007 0.001 TYR H 100 ARG 0.003 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 60) link_NAG-ASN : angle 1.93287 ( 180) link_ALPHA1-6 : bond 0.00788 ( 2) link_ALPHA1-6 : angle 1.31959 ( 6) link_BETA1-4 : bond 0.00903 ( 54) link_BETA1-4 : angle 2.76981 ( 162) link_ALPHA1-2 : bond 0.00700 ( 1) link_ALPHA1-2 : angle 2.91637 ( 3) link_ALPHA1-3 : bond 0.00875 ( 3) link_ALPHA1-3 : angle 2.57204 ( 9) hydrogen bonds : bond 0.03872 ( 556) hydrogen bonds : angle 4.90037 ( 1551) SS BOND : bond 0.00318 ( 34) SS BOND : angle 0.84859 ( 68) covalent geometry : bond 0.00396 (17072) covalent geometry : angle 0.59940 (23182) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9466 (ttm) cc_final: 0.9148 (ttm) REVERT: A 257 THR cc_start: 0.9405 (OUTLIER) cc_final: 0.9078 (p) REVERT: A 426 MET cc_start: 0.8187 (ptm) cc_final: 0.7440 (ppp) REVERT: A 475 MET cc_start: 0.8765 (mmm) cc_final: 0.8302 (mmm) REVERT: B 647 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8335 (mt-10) REVERT: B 657 GLU cc_start: 0.9191 (tt0) cc_final: 0.8737 (tm-30) REVERT: C 95 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8075 (ptt) REVERT: E 102 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8506 (tm-30) REVERT: E 475 MET cc_start: 0.9411 (tpt) cc_final: 0.9204 (tpp) REVERT: F 648 GLU cc_start: 0.9227 (pt0) cc_final: 0.8945 (pp20) REVERT: G 530 MET cc_start: 0.8755 (ttm) cc_final: 0.8529 (ttm) REVERT: G 657 GLU cc_start: 0.9051 (tt0) cc_final: 0.8797 (pp20) REVERT: H 34 MET cc_start: 0.9226 (tpp) cc_final: 0.8343 (mmm) REVERT: H 46 GLU cc_start: 0.8943 (tt0) cc_final: 0.8604 (tt0) REVERT: H 100 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7898 (tp30) REVERT: H 108 ARG cc_start: 0.8689 (mmt90) cc_final: 0.8284 (tpt-90) REVERT: L 18 ARG cc_start: 0.9129 (ttt90) cc_final: 0.8903 (tpp80) REVERT: L 105 ASP cc_start: 0.8813 (t0) cc_final: 0.8354 (p0) outliers start: 25 outliers final: 13 residues processed: 90 average time/residue: 0.2647 time to fit residues: 39.3083 Evaluate side-chains 79 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain G residue 639 THR Chi-restraints excluded: chain H residue 78 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 59 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.043995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.034073 restraints weight = 107046.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.035331 restraints weight = 55459.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.036079 restraints weight = 37664.376| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17226 Z= 0.182 Angle : 0.662 16.908 23610 Z= 0.301 Chirality : 0.045 0.404 2962 Planarity : 0.003 0.037 2771 Dihedral : 8.689 62.725 4516 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.60 % Allowed : 12.06 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.19), residues: 1864 helix: 1.51 (0.26), residues: 402 sheet: -0.38 (0.22), residues: 536 loop : -1.12 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 53 HIS 0.004 0.001 HIS E 249 PHE 0.009 0.001 PHE L 83 TYR 0.012 0.001 TYR H 100 ARG 0.002 0.000 ARG E 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 60) link_NAG-ASN : angle 1.88804 ( 180) link_ALPHA1-6 : bond 0.00788 ( 2) link_ALPHA1-6 : angle 1.29661 ( 6) link_BETA1-4 : bond 0.00893 ( 54) link_BETA1-4 : angle 2.69808 ( 162) link_ALPHA1-2 : bond 0.00673 ( 1) link_ALPHA1-2 : angle 2.78970 ( 3) link_ALPHA1-3 : bond 0.00817 ( 3) link_ALPHA1-3 : angle 2.55252 ( 9) hydrogen bonds : bond 0.03730 ( 556) hydrogen bonds : angle 4.81913 ( 1551) SS BOND : bond 0.00316 ( 34) SS BOND : angle 0.83688 ( 68) covalent geometry : bond 0.00402 (17072) covalent geometry : angle 0.60144 (23182) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9475 (ttm) cc_final: 0.9145 (ttm) REVERT: A 184 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8943 (tp) REVERT: A 257 THR cc_start: 0.9410 (OUTLIER) cc_final: 0.9084 (p) REVERT: A 475 MET cc_start: 0.8699 (mmm) cc_final: 0.8330 (mmm) REVERT: B 647 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8338 (mt-10) REVERT: B 657 GLU cc_start: 0.9201 (tt0) cc_final: 0.8720 (tm-30) REVERT: E 102 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8556 (tm-30) REVERT: F 648 GLU cc_start: 0.9257 (pt0) cc_final: 0.8961 (pp20) REVERT: G 530 MET cc_start: 0.8701 (ttm) cc_final: 0.8466 (ttm) REVERT: G 657 GLU cc_start: 0.9078 (tt0) cc_final: 0.8829 (pp20) REVERT: H 46 GLU cc_start: 0.8939 (tt0) cc_final: 0.8601 (tt0) REVERT: H 100 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7857 (tp30) REVERT: H 108 ARG cc_start: 0.8738 (mmt90) cc_final: 0.8234 (tpt-90) REVERT: L 105 ASP cc_start: 0.8874 (t0) cc_final: 0.8406 (p0) REVERT: L 106 ILE cc_start: 0.7395 (mp) cc_final: 0.7190 (mp) outliers start: 27 outliers final: 17 residues processed: 92 average time/residue: 0.2585 time to fit residues: 40.1267 Evaluate side-chains 84 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain L residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 90 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 182 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN F 585 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.043357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.033266 restraints weight = 104769.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.034497 restraints weight = 53913.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.035339 restraints weight = 36616.977| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17226 Z= 0.255 Angle : 0.712 16.911 23610 Z= 0.325 Chirality : 0.045 0.404 2962 Planarity : 0.004 0.041 2771 Dihedral : 8.909 63.749 4516 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.30 % Allowed : 12.12 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.19), residues: 1864 helix: 1.47 (0.26), residues: 402 sheet: -0.41 (0.22), residues: 526 loop : -1.14 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 53 HIS 0.005 0.001 HIS E 330 PHE 0.015 0.002 PHE C 376 TYR 0.012 0.001 TYR B 638 ARG 0.003 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 60) link_NAG-ASN : angle 2.02845 ( 180) link_ALPHA1-6 : bond 0.00689 ( 2) link_ALPHA1-6 : angle 1.29589 ( 6) link_BETA1-4 : bond 0.00878 ( 54) link_BETA1-4 : angle 2.71832 ( 162) link_ALPHA1-2 : bond 0.00873 ( 1) link_ALPHA1-2 : angle 2.99238 ( 3) link_ALPHA1-3 : bond 0.00847 ( 3) link_ALPHA1-3 : angle 2.52101 ( 9) hydrogen bonds : bond 0.03879 ( 556) hydrogen bonds : angle 4.91570 ( 1551) SS BOND : bond 0.00384 ( 34) SS BOND : angle 0.98412 ( 68) covalent geometry : bond 0.00563 (17072) covalent geometry : angle 0.65261 (23182) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 65 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9477 (ttm) cc_final: 0.9134 (ttm) REVERT: A 184 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8868 (tp) REVERT: A 257 THR cc_start: 0.9455 (OUTLIER) cc_final: 0.9175 (p) REVERT: A 426 MET cc_start: 0.8373 (ptm) cc_final: 0.7740 (ppp) REVERT: A 475 MET cc_start: 0.8668 (mmm) cc_final: 0.8146 (mmm) REVERT: A 478 ASN cc_start: 0.9341 (OUTLIER) cc_final: 0.9101 (m-40) REVERT: B 647 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8300 (mt-10) REVERT: B 657 GLU cc_start: 0.9182 (tt0) cc_final: 0.8720 (tm-30) REVERT: C 161 MET cc_start: 0.8779 (mmm) cc_final: 0.8433 (tpt) REVERT: F 585 HIS cc_start: 0.8470 (OUTLIER) cc_final: 0.8153 (t70) REVERT: G 657 GLU cc_start: 0.9043 (tt0) cc_final: 0.8833 (pp20) REVERT: H 34 MET cc_start: 0.9137 (tpp) cc_final: 0.8345 (mmm) REVERT: H 46 GLU cc_start: 0.8959 (tt0) cc_final: 0.8625 (tt0) REVERT: H 100 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7759 (tp30) REVERT: H 108 ARG cc_start: 0.8757 (mmt90) cc_final: 0.8366 (tpt-90) REVERT: L 105 ASP cc_start: 0.8911 (t0) cc_final: 0.8427 (p0) outliers start: 39 outliers final: 23 residues processed: 101 average time/residue: 0.2587 time to fit residues: 43.2497 Evaluate side-chains 90 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 352 TYR Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 427 TRP Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain F residue 585 HIS Chi-restraints excluded: chain G residue 639 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 129 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 HIS E 103 GLN E 377 ASN F 585 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.043745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.033709 restraints weight = 103768.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.034942 restraints weight = 52796.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.035709 restraints weight = 35955.797| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17226 Z= 0.188 Angle : 0.673 16.775 23610 Z= 0.309 Chirality : 0.045 0.406 2962 Planarity : 0.003 0.039 2771 Dihedral : 8.793 62.057 4516 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.95 % Allowed : 12.77 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.19), residues: 1864 helix: 1.45 (0.26), residues: 402 sheet: -0.37 (0.23), residues: 526 loop : -1.13 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 53 HIS 0.006 0.001 HIS F 585 PHE 0.012 0.001 PHE L 83 TYR 0.012 0.001 TYR H 100 ARG 0.002 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 60) link_NAG-ASN : angle 1.89689 ( 180) link_ALPHA1-6 : bond 0.00759 ( 2) link_ALPHA1-6 : angle 1.30216 ( 6) link_BETA1-4 : bond 0.00893 ( 54) link_BETA1-4 : angle 2.65485 ( 162) link_ALPHA1-2 : bond 0.00749 ( 1) link_ALPHA1-2 : angle 2.78828 ( 3) link_ALPHA1-3 : bond 0.00805 ( 3) link_ALPHA1-3 : angle 2.56877 ( 9) hydrogen bonds : bond 0.03718 ( 556) hydrogen bonds : angle 4.84038 ( 1551) SS BOND : bond 0.00346 ( 34) SS BOND : angle 0.89358 ( 68) covalent geometry : bond 0.00416 (17072) covalent geometry : angle 0.61480 (23182) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 64 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9479 (ttm) cc_final: 0.9157 (ttm) REVERT: A 184 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8854 (tp) REVERT: A 257 THR cc_start: 0.9430 (OUTLIER) cc_final: 0.9144 (p) REVERT: A 426 MET cc_start: 0.8264 (ptm) cc_final: 0.7682 (ppp) REVERT: A 475 MET cc_start: 0.8611 (mmm) cc_final: 0.8141 (mmm) REVERT: A 478 ASN cc_start: 0.9300 (OUTLIER) cc_final: 0.9086 (m-40) REVERT: B 647 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8320 (mt-10) REVERT: C 161 MET cc_start: 0.8763 (mmm) cc_final: 0.8422 (tpt) REVERT: F 648 GLU cc_start: 0.9226 (pt0) cc_final: 0.8943 (pp20) REVERT: G 530 MET cc_start: 0.8538 (ttm) cc_final: 0.8125 (tpp) REVERT: G 657 GLU cc_start: 0.9064 (tt0) cc_final: 0.8845 (pp20) REVERT: H 46 GLU cc_start: 0.8962 (tt0) cc_final: 0.8621 (tt0) REVERT: H 100 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7755 (tp30) REVERT: H 108 ARG cc_start: 0.8768 (mmt90) cc_final: 0.8256 (tpt-90) REVERT: L 105 ASP cc_start: 0.8934 (t0) cc_final: 0.8363 (p0) outliers start: 33 outliers final: 24 residues processed: 95 average time/residue: 0.2435 time to fit residues: 39.3256 Evaluate side-chains 89 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 352 TYR Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain G residue 639 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 131 optimal weight: 0.9980 chunk 86 optimal weight: 0.2980 chunk 40 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 186 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS E 377 ASN F 585 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.044638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.034810 restraints weight = 105384.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.036108 restraints weight = 54108.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.036868 restraints weight = 36323.775| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17226 Z= 0.113 Angle : 0.635 16.962 23610 Z= 0.291 Chirality : 0.045 0.402 2962 Planarity : 0.003 0.041 2771 Dihedral : 8.476 57.716 4516 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.65 % Allowed : 13.12 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.19), residues: 1864 helix: 1.64 (0.26), residues: 402 sheet: -0.28 (0.23), residues: 530 loop : -1.09 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 631 HIS 0.006 0.001 HIS E 374 PHE 0.011 0.001 PHE C 383 TYR 0.012 0.001 TYR B 638 ARG 0.002 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 60) link_NAG-ASN : angle 1.68029 ( 180) link_ALPHA1-6 : bond 0.00925 ( 2) link_ALPHA1-6 : angle 1.30046 ( 6) link_BETA1-4 : bond 0.00928 ( 54) link_BETA1-4 : angle 2.58684 ( 162) link_ALPHA1-2 : bond 0.00575 ( 1) link_ALPHA1-2 : angle 2.63119 ( 3) link_ALPHA1-3 : bond 0.00695 ( 3) link_ALPHA1-3 : angle 2.63773 ( 9) hydrogen bonds : bond 0.03470 ( 556) hydrogen bonds : angle 4.69981 ( 1551) SS BOND : bond 0.00258 ( 34) SS BOND : angle 0.88950 ( 68) covalent geometry : bond 0.00241 (17072) covalent geometry : angle 0.57927 (23182) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8792 (tp) REVERT: A 426 MET cc_start: 0.8148 (ptm) cc_final: 0.7561 (ppp) REVERT: A 475 MET cc_start: 0.8557 (mmm) cc_final: 0.8248 (mmm) REVERT: B 647 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8360 (mt-10) REVERT: C 161 MET cc_start: 0.8773 (mmm) cc_final: 0.8497 (tpt) REVERT: F 648 GLU cc_start: 0.9202 (pt0) cc_final: 0.8922 (pp20) REVERT: F 652 GLN cc_start: 0.9096 (tp40) cc_final: 0.8761 (tp40) REVERT: G 657 GLU cc_start: 0.9071 (tt0) cc_final: 0.8855 (pp20) REVERT: H 46 GLU cc_start: 0.8992 (tt0) cc_final: 0.8673 (tt0) REVERT: H 82 MET cc_start: 0.8563 (mmm) cc_final: 0.8241 (mmm) REVERT: H 100 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7655 (tp30) REVERT: H 108 ARG cc_start: 0.8792 (mmt90) cc_final: 0.8311 (tpt-90) REVERT: L 18 ARG cc_start: 0.9141 (ttt90) cc_final: 0.8870 (tpp80) REVERT: L 105 ASP cc_start: 0.8881 (t0) cc_final: 0.8287 (p0) outliers start: 28 outliers final: 21 residues processed: 94 average time/residue: 0.3513 time to fit residues: 55.1200 Evaluate side-chains 87 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 352 TYR Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain F residue 585 HIS Chi-restraints excluded: chain G residue 639 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 144 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN F 585 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.044829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.034858 restraints weight = 103565.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.036154 restraints weight = 53398.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.036997 restraints weight = 35986.103| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17226 Z= 0.115 Angle : 0.627 16.863 23610 Z= 0.287 Chirality : 0.044 0.398 2962 Planarity : 0.003 0.037 2771 Dihedral : 8.391 57.047 4516 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.30 % Allowed : 13.36 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1864 helix: 1.67 (0.26), residues: 402 sheet: -0.27 (0.22), residues: 541 loop : -1.07 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 631 HIS 0.008 0.001 HIS C 374 PHE 0.014 0.001 PHE C 376 TYR 0.011 0.001 TYR B 638 ARG 0.002 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 60) link_NAG-ASN : angle 1.65893 ( 180) link_ALPHA1-6 : bond 0.00895 ( 2) link_ALPHA1-6 : angle 1.28588 ( 6) link_BETA1-4 : bond 0.00909 ( 54) link_BETA1-4 : angle 2.56657 ( 162) link_ALPHA1-2 : bond 0.00549 ( 1) link_ALPHA1-2 : angle 2.65833 ( 3) link_ALPHA1-3 : bond 0.00753 ( 3) link_ALPHA1-3 : angle 2.57764 ( 9) hydrogen bonds : bond 0.03363 ( 556) hydrogen bonds : angle 4.66998 ( 1551) SS BOND : bond 0.00251 ( 34) SS BOND : angle 0.68692 ( 68) covalent geometry : bond 0.00250 (17072) covalent geometry : angle 0.57200 (23182) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9460 (ttm) cc_final: 0.9143 (ttm) REVERT: A 426 MET cc_start: 0.8169 (ptm) cc_final: 0.7555 (ppp) REVERT: A 475 MET cc_start: 0.8546 (mmm) cc_final: 0.8288 (mmm) REVERT: B 647 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8341 (mt-10) REVERT: C 161 MET cc_start: 0.8729 (mmm) cc_final: 0.8460 (tpt) REVERT: F 648 GLU cc_start: 0.9178 (pt0) cc_final: 0.8903 (pp20) REVERT: F 652 GLN cc_start: 0.9073 (tp40) cc_final: 0.8728 (tp40) REVERT: G 657 GLU cc_start: 0.9059 (tt0) cc_final: 0.8777 (tm-30) REVERT: H 46 GLU cc_start: 0.9004 (tt0) cc_final: 0.8649 (tt0) REVERT: H 82 MET cc_start: 0.8501 (mmm) cc_final: 0.8206 (mmm) REVERT: H 100 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7637 (tp30) REVERT: H 108 ARG cc_start: 0.8800 (mmt90) cc_final: 0.8323 (tpt-90) REVERT: L 105 ASP cc_start: 0.8922 (t0) cc_final: 0.8337 (p0) outliers start: 22 outliers final: 19 residues processed: 88 average time/residue: 0.2748 time to fit residues: 39.8199 Evaluate side-chains 83 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain G residue 639 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 89 optimal weight: 0.0570 chunk 131 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 170 optimal weight: 0.4980 chunk 124 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.045186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.035311 restraints weight = 102433.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.036613 restraints weight = 52620.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.037469 restraints weight = 35297.789| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17226 Z= 0.105 Angle : 0.615 16.926 23610 Z= 0.281 Chirality : 0.044 0.400 2962 Planarity : 0.003 0.036 2771 Dihedral : 8.211 56.807 4516 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.30 % Allowed : 13.42 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.20), residues: 1864 helix: 1.76 (0.26), residues: 402 sheet: -0.27 (0.22), residues: 553 loop : -1.03 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 623 HIS 0.008 0.001 HIS C 374 PHE 0.018 0.001 PHE C 383 TYR 0.011 0.001 TYR B 638 ARG 0.004 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 60) link_NAG-ASN : angle 1.59221 ( 180) link_ALPHA1-6 : bond 0.00932 ( 2) link_ALPHA1-6 : angle 1.28763 ( 6) link_BETA1-4 : bond 0.00930 ( 54) link_BETA1-4 : angle 2.52545 ( 162) link_ALPHA1-2 : bond 0.00494 ( 1) link_ALPHA1-2 : angle 2.56562 ( 3) link_ALPHA1-3 : bond 0.00725 ( 3) link_ALPHA1-3 : angle 2.58732 ( 9) hydrogen bonds : bond 0.03234 ( 556) hydrogen bonds : angle 4.58453 ( 1551) SS BOND : bond 0.00234 ( 34) SS BOND : angle 0.64829 ( 68) covalent geometry : bond 0.00225 (17072) covalent geometry : angle 0.56225 (23182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4844.28 seconds wall clock time: 86 minutes 59.59 seconds (5219.59 seconds total)