Starting phenix.real_space_refine on Sat Jul 4 02:50:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zry_74655/07_2026/9zry_74655.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zry_74655/07_2026/9zry_74655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zry_74655/07_2026/9zry_74655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zry_74655/07_2026/9zry_74655.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zry_74655/07_2026/9zry_74655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zry_74655/07_2026/9zry_74655.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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 111 5.16 5 C 10752 2.51 5 N 2842 2.21 5 O 3543 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17248 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1005 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 2, 'TRANS': 127} 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: "B" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 886 Classifications: {'peptide': 115} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 105} Chain: "b" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3525 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "c" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1026 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "d" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3525 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "e" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1026 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "f" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3525 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "g" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1026 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 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: 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: "j" 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: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "e" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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 Time building chain proxies: 4.28, per 1000 atoms: 0.25 Number of scatterers: 17248 At special positions: 0 Unit cell: (134.46, 132.8, 166, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 3543 8.00 N 2842 7.00 C 10752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS b 54 " - pdb=" SG CYS b 74 " distance=2.03 Simple disulfide: pdb=" SG CYS b 119 " - pdb=" SG CYS b 205 " distance=2.03 Simple disulfide: pdb=" SG CYS b 126 " - pdb=" SG CYS b 196 " distance=2.03 Simple disulfide: pdb=" SG CYS b 131 " - pdb=" SG CYS b 157 " distance=2.03 Simple disulfide: pdb=" SG CYS b 201 " - pdb=" SG CYS b 433 " distance=2.03 Simple disulfide: pdb=" SG CYS b 218 " - pdb=" SG CYS b 247 " distance=2.03 Simple disulfide: pdb=" SG CYS b 228 " - pdb=" SG CYS b 239 " distance=2.03 Simple disulfide: pdb=" SG CYS b 296 " - pdb=" SG CYS b 331 " distance=2.03 Simple disulfide: pdb=" SG CYS b 378 " - pdb=" SG CYS b 445 " distance=2.04 Simple disulfide: pdb=" SG CYS b 385 " - pdb=" SG CYS b 418 " distance=2.03 Simple disulfide: pdb=" SG CYS b 501 " - pdb=" SG CYS c 605 " distance=2.03 Simple disulfide: pdb=" SG CYS c 598 " - pdb=" SG CYS c 604 " distance=2.03 Simple disulfide: pdb=" SG CYS d 54 " - pdb=" SG CYS d 74 " distance=2.03 Simple disulfide: pdb=" SG CYS d 119 " - pdb=" SG CYS d 205 " distance=2.03 Simple disulfide: pdb=" SG CYS d 126 " - pdb=" SG CYS d 196 " distance=2.03 Simple disulfide: pdb=" SG CYS d 131 " - pdb=" SG CYS d 157 " distance=2.03 Simple disulfide: pdb=" SG CYS d 201 " - pdb=" SG CYS d 433 " distance=2.03 Simple disulfide: pdb=" SG CYS d 218 " - pdb=" SG CYS d 247 " distance=2.03 Simple disulfide: pdb=" SG CYS d 228 " - pdb=" SG CYS d 239 " distance=2.03 Simple disulfide: pdb=" SG CYS d 296 " - pdb=" SG CYS d 331 " distance=2.03 Simple disulfide: pdb=" SG CYS d 378 " - pdb=" SG CYS d 445 " distance=2.04 Simple disulfide: pdb=" SG CYS d 385 " - pdb=" SG CYS d 418 " distance=2.03 Simple disulfide: pdb=" SG CYS d 501 " - pdb=" SG CYS e 605 " distance=2.03 Simple disulfide: pdb=" SG CYS e 598 " - pdb=" SG CYS e 604 " distance=2.03 Simple disulfide: pdb=" SG CYS f 54 " - pdb=" SG CYS f 74 " distance=2.04 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 205 " distance=2.03 Simple disulfide: pdb=" SG CYS f 126 " - pdb=" SG CYS f 196 " distance=2.03 Simple disulfide: pdb=" SG CYS f 131 " - pdb=" SG CYS f 157 " distance=2.03 Simple disulfide: pdb=" SG CYS f 201 " - pdb=" SG CYS f 433 " distance=2.03 Simple disulfide: pdb=" SG CYS f 218 " - pdb=" SG CYS f 247 " distance=2.03 Simple disulfide: pdb=" SG CYS f 228 " - pdb=" SG CYS f 239 " distance=2.03 Simple disulfide: pdb=" SG CYS f 296 " - pdb=" SG CYS f 331 " distance=2.03 Simple disulfide: pdb=" SG CYS f 378 " - pdb=" SG CYS f 445 " distance=2.04 Simple disulfide: pdb=" SG CYS f 385 " - pdb=" SG CYS f 418 " distance=2.03 Simple disulfide: pdb=" SG CYS f 501 " - pdb=" SG CYS g 605 " distance=2.03 Simple disulfide: pdb=" SG CYS g 598 " - pdb=" SG CYS g 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA G 3 " - " MAN G 4 " " BMA Q 3 " - " MAN Q 4 " " BMA j 3 " - " MAN j 4 " " BMA l 3 " - " MAN l 7 " " MAN l 4 " - " MAN l 5 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA Q 3 " - " MAN Q 5 " " BMA j 3 " - " MAN j 5 " " BMA l 3 " - " MAN l 4 " " MAN l 4 " - " MAN l 6 " BETA1-4 " 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 E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " 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 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG 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 q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " NAG-ASN " NAG C 1 " - " ASN b 392 " " NAG D 1 " - " ASN b 332 " " NAG E 1 " - " ASN b 262 " " NAG F 1 " - " ASN b 156 " " NAG G 1 " - " ASN b 160 " " NAG H 1 " - " ASN b 197 " " NAG I 1 " - " ASN b 234 " " NAG J 1 " - " ASN b 241 " " NAG K 1 " - " ASN b 276 " " NAG L 1 " - " ASN b 301 " " NAG M 1 " - " ASN b 448 " " NAG N 1 " - " ASN b 465 " " NAG O 1 " - " ASN d 392 " " NAG P 1 " - " ASN d 332 " " NAG Q 1 " - " ASN d 262 " " NAG R 1 " - " ASN d 156 " " NAG S 1 " - " ASN d 197 " " NAG T 1 " - " ASN d 234 " " NAG U 1 " - " ASN d 241 " " NAG V 1 " - " ASN d 276 " " NAG W 1 " - " ASN d 301 " " NAG Z 1 " - " ASN d 448 " " NAG a 1 " - " ASN d 465 " " NAG b 601 " - " ASN b 88 " " NAG b 602 " - " ASN b 133 " " NAG b 603 " - " ASN b 339 " " NAG b 604 " - " ASN b 355 " " NAG b 605 " - " ASN b 269 " " NAG b 606 " - " ASN b 363 " " NAG b 607 " - " ASN b 386 " " NAG b 608 " - " ASN b 398 " " NAG c 701 " - " ASN c 611 " " NAG c 702 " - " ASN c 637 " " NAG c 703 " - " ASN c 625 " " NAG d 601 " - " ASN d 88 " " NAG d 602 " - " ASN d 133 " " NAG d 603 " - " ASN d 160 " " NAG d 604 " - " ASN d 355 " " NAG d 605 " - " ASN d 269 " " NAG d 606 " - " ASN d 339 " " NAG d 607 " - " ASN d 398 " " NAG e 701 " - " ASN e 611 " " NAG e 702 " - " ASN e 637 " " NAG e 703 " - " ASN e 625 " " NAG f 601 " - " ASN f 88 " " NAG f 602 " - " ASN f 133 " " NAG f 603 " - " ASN f 339 " " NAG f 604 " - " ASN f 355 " " NAG f 605 " - " ASN f 269 " " NAG f 606 " - " ASN f 398 " " NAG f 607 " - " ASN f 386 " " NAG f 608 " - " ASN f 363 " " NAG g 701 " - " ASN g 611 " " NAG g 702 " - " ASN g 637 " " NAG g 703 " - " ASN g 625 " " NAG h 1 " - " ASN f 392 " " NAG i 1 " - " ASN f 332 " " NAG j 1 " - " ASN f 262 " " NAG k 1 " - " ASN f 156 " " NAG l 1 " - " ASN f 160 " " NAG m 1 " - " ASN f 197 " " NAG n 1 " - " ASN f 234 " " NAG o 1 " - " ASN f 241 " " NAG p 1 " - " ASN f 276 " " NAG q 1 " - " ASN f 301 " " NAG r 1 " - " ASN f 448 " " NAG s 1 " - " ASN f 465 " Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 704.2 milliseconds 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3650 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 36 sheets defined 24.1% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 28 through 30 No H-bonds generated for 'chain 'A' and resid 28 through 30' Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'B' and resid 85 through 89 removed outlier: 3.983A pdb=" N VAL B 89 " --> pdb=" O ALA B 86 " (cutoff:3.500A) Processing helix chain 'b' and resid 70 through 74 Processing helix chain 'b' and resid 98 through 117 removed outlier: 4.303A pdb=" N GLU b 102 " --> pdb=" O ASN b 98 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 126 Processing helix chain 'b' and resid 334 through 351 removed outlier: 3.655A pdb=" N THR b 341 " --> pdb=" O ARG b 337 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR b 351 " --> pdb=" O GLU b 347 " (cutoff:3.500A) Processing helix chain 'b' and resid 387 through 390 Processing helix chain 'b' and resid 475 through 481 removed outlier: 3.805A pdb=" N TRP b 479 " --> pdb=" O MET b 475 " (cutoff:3.500A) Processing helix chain 'b' and resid 482 through 484 No H-bonds generated for 'chain 'b' and resid 482 through 484' Processing helix chain 'c' and resid 523 through 527 removed outlier: 3.645A pdb=" N ALA c 526 " --> pdb=" O LEU c 523 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY c 527 " --> pdb=" O GLY c 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 523 through 527' Processing helix chain 'c' and resid 529 through 534 Processing helix chain 'c' and resid 536 through 543 removed outlier: 3.744A pdb=" N GLN c 540 " --> pdb=" O THR c 536 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN c 543 " --> pdb=" O VAL c 539 " (cutoff:3.500A) Processing helix chain 'c' and resid 544 through 546 No H-bonds generated for 'chain 'c' and resid 544 through 546' Processing helix chain 'c' and resid 569 through 596 removed outlier: 3.501A pdb=" N ASP c 589 " --> pdb=" O ARG c 585 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU c 592 " --> pdb=" O ARG c 588 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU c 593 " --> pdb=" O ASP c 589 " (cutoff:3.500A) Processing helix chain 'c' and resid 619 through 625 removed outlier: 3.784A pdb=" N TRP c 623 " --> pdb=" O LEU c 619 " (cutoff:3.500A) Processing helix chain 'c' and resid 627 through 636 removed outlier: 4.056A pdb=" N LYS c 633 " --> pdb=" O LEU c 629 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU c 634 " --> pdb=" O GLN c 630 " (cutoff:3.500A) Processing helix chain 'c' and resid 638 through 658 Processing helix chain 'd' and resid 70 through 74 Processing helix chain 'd' and resid 98 through 117 removed outlier: 4.289A pdb=" N GLU d 102 " --> pdb=" O ASN d 98 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR d 106 " --> pdb=" O GLU d 102 " (cutoff:3.500A) Processing helix chain 'd' and resid 122 through 126 Processing helix chain 'd' and resid 334 through 351 removed outlier: 4.027A pdb=" N LYS d 340 " --> pdb=" O SER d 336 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR d 351 " --> pdb=" O GLU d 347 " (cutoff:3.500A) Processing helix chain 'd' and resid 352 through 354 No H-bonds generated for 'chain 'd' and resid 352 through 354' Processing helix chain 'd' and resid 368 through 373 Processing helix chain 'd' and resid 475 through 484 removed outlier: 4.002A pdb=" N TRP d 479 " --> pdb=" O MET d 475 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU d 482 " --> pdb=" O ASN d 478 " (cutoff:3.500A) Processing helix chain 'e' and resid 523 through 527 removed outlier: 3.622A pdb=" N ALA e 526 " --> pdb=" O LEU e 523 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY e 527 " --> pdb=" O GLY e 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 523 through 527' Processing helix chain 'e' and resid 529 through 534 Processing helix chain 'e' and resid 536 through 543 removed outlier: 3.739A pdb=" N GLN e 540 " --> pdb=" O THR e 536 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN e 543 " --> pdb=" O VAL e 539 " (cutoff:3.500A) Processing helix chain 'e' and resid 544 through 546 No H-bonds generated for 'chain 'e' and resid 544 through 546' Processing helix chain 'e' and resid 569 through 596 removed outlier: 3.873A pdb=" N LEU e 592 " --> pdb=" O ARG e 588 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU e 593 " --> pdb=" O ASP e 589 " (cutoff:3.500A) Processing helix chain 'e' and resid 618 through 625 removed outlier: 3.683A pdb=" N TRP e 623 " --> pdb=" O LEU e 619 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN e 624 " --> pdb=" O ASP e 620 " (cutoff:3.500A) Processing helix chain 'e' and resid 627 through 636 removed outlier: 4.094A pdb=" N LYS e 633 " --> pdb=" O LEU e 629 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU e 634 " --> pdb=" O GLN e 630 " (cutoff:3.500A) Processing helix chain 'e' and resid 638 through 658 Processing helix chain 'f' and resid 70 through 74 Processing helix chain 'f' and resid 98 through 117 removed outlier: 4.269A pdb=" N GLU f 102 " --> pdb=" O ASN f 98 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR f 106 " --> pdb=" O GLU f 102 " (cutoff:3.500A) Processing helix chain 'f' and resid 122 through 126 Processing helix chain 'f' and resid 334 through 351 Processing helix chain 'f' and resid 368 through 373 Processing helix chain 'f' and resid 387 through 390 Processing helix chain 'f' and resid 475 through 481 removed outlier: 3.837A pdb=" N TRP f 479 " --> pdb=" O MET f 475 " (cutoff:3.500A) Processing helix chain 'f' and resid 482 through 484 No H-bonds generated for 'chain 'f' and resid 482 through 484' Processing helix chain 'g' and resid 529 through 534 Processing helix chain 'g' and resid 536 through 543 removed outlier: 3.937A pdb=" N GLN g 540 " --> pdb=" O THR g 536 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN g 543 " --> pdb=" O VAL g 539 " (cutoff:3.500A) Processing helix chain 'g' and resid 544 through 546 No H-bonds generated for 'chain 'g' and resid 544 through 546' Processing helix chain 'g' and resid 569 through 596 removed outlier: 3.527A pdb=" N ASP g 589 " --> pdb=" O ARG g 585 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU g 592 " --> pdb=" O ARG g 588 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU g 593 " --> pdb=" O ASP g 589 " (cutoff:3.500A) Processing helix chain 'g' and resid 618 through 625 removed outlier: 3.822A pdb=" N TRP g 623 " --> pdb=" O LEU g 619 " (cutoff:3.500A) Processing helix chain 'g' and resid 627 through 658 removed outlier: 4.174A pdb=" N LYS g 633 " --> pdb=" O LEU g 629 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU g 634 " --> pdb=" O GLN g 630 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE g 635 " --> pdb=" O TRP g 631 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASN g 637 " --> pdb=" O LYS g 633 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR g 638 " --> pdb=" O GLU g 634 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLN g 640 " --> pdb=" O GLY g 636 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU g 641 " --> pdb=" O ASN g 637 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG g 644 " --> pdb=" O GLN g 640 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU g 647 " --> pdb=" O TYR g 643 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU g 648 " --> pdb=" O ARG g 644 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.896A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLY A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N MET A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER A 119 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.670A pdb=" N GLY B 90 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 54 " --> pdb=" O TRP B 41 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU B 43 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU B 52 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 494 through 499 removed outlier: 5.369A pdb=" N VAL c 608 " --> pdb=" O VAL b 36 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL b 38 " --> pdb=" O THR c 606 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR c 606 " --> pdb=" O VAL b 38 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N TYR b 40 " --> pdb=" O CYS c 604 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N CYS c 604 " --> pdb=" O TYR b 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 45 through 47 removed outlier: 4.803A pdb=" N VAL b 242 " --> pdb=" O LEU b 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 53 through 55 Processing sheet with id=AA9, first strand: chain 'b' and resid 66 through 67 removed outlier: 7.004A pdb=" N HIS b 66 " --> pdb=" O SER b 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'b' and resid 91 through 94 Processing sheet with id=AB2, first strand: chain 'b' and resid 130 through 133 Processing sheet with id=AB3, first strand: chain 'b' and resid 181 through 183 Processing sheet with id=AB4, first strand: chain 'b' and resid 202 through 203 removed outlier: 6.381A pdb=" N THR b 202 " --> pdb=" O TYR b 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'b' and resid 259 through 261 removed outlier: 10.035A pdb=" N LYS b 444 " --> pdb=" O ILE b 294 " (cutoff:3.500A) removed outlier: 11.390A pdb=" N ILE b 294 " --> pdb=" O LYS b 444 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N GLU b 446 " --> pdb=" O VAL b 292 " (cutoff:3.500A) removed outlier: 10.685A pdb=" N VAL b 292 " --> pdb=" O GLU b 446 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N ASN b 448 " --> pdb=" O GLN b 290 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N GLN b 290 " --> pdb=" O ASN b 448 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR b 450 " --> pdb=" O LEU b 288 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS b 330 " --> pdb=" O ILE b 297 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA b 329 " --> pdb=" O CYS b 418 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS b 421 " --> pdb=" O PHE b 382 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE b 382 " --> pdb=" O LYS b 421 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'b' and resid 271 through 273 removed outlier: 6.556A pdb=" N THR b 450 " --> pdb=" O LEU b 288 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N GLN b 290 " --> pdb=" O ASN b 448 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N ASN b 448 " --> pdb=" O GLN b 290 " (cutoff:3.500A) removed outlier: 10.685A pdb=" N VAL b 292 " --> pdb=" O GLU b 446 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N GLU b 446 " --> pdb=" O VAL b 292 " (cutoff:3.500A) removed outlier: 11.390A pdb=" N ILE b 294 " --> pdb=" O LYS b 444 " (cutoff:3.500A) removed outlier: 10.035A pdb=" N LYS b 444 " --> pdb=" O ILE b 294 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR b 357 " --> pdb=" O GLU b 466 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE b 468 " --> pdb=" O THR b 357 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE b 359 " --> pdb=" O PHE b 468 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER b 393 " --> pdb=" O PHE b 361 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 301 through 312 removed outlier: 7.028A pdb=" N ASN b 301 " --> pdb=" O ILE b 323 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ILE b 323 " --> pdb=" O ASN b 301 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR b 303 " --> pdb=" O GLY b 321 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLN b 315 " --> pdb=" O ILE b 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'd' and resid 494 through 499 removed outlier: 5.405A pdb=" N VAL e 608 " --> pdb=" O VAL d 36 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N VAL d 38 " --> pdb=" O THR e 606 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N THR e 606 " --> pdb=" O VAL d 38 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N TYR d 40 " --> pdb=" O CYS e 604 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N CYS e 604 " --> pdb=" O TYR d 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'd' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'd' and resid 66 through 67 removed outlier: 7.259A pdb=" N HIS d 66 " --> pdb=" O SER d 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'd' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'd' and resid 130 through 133 Processing sheet with id=AC4, first strand: chain 'd' and resid 181 through 183 Processing sheet with id=AC5, first strand: chain 'd' and resid 202 through 203 removed outlier: 6.314A pdb=" N THR d 202 " --> pdb=" O TYR d 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'd' and resid 259 through 261 removed outlier: 3.522A pdb=" N GLY d 451 " --> pdb=" O LEU d 260 " (cutoff:3.500A) removed outlier: 10.163A pdb=" N LYS d 444 " --> pdb=" O ILE d 294 " (cutoff:3.500A) removed outlier: 11.496A pdb=" N ILE d 294 " --> pdb=" O LYS d 444 " (cutoff:3.500A) removed outlier: 9.860A pdb=" N GLU d 446 " --> pdb=" O VAL d 292 " (cutoff:3.500A) removed outlier: 10.767A pdb=" N VAL d 292 " --> pdb=" O GLU d 446 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ASN d 448 " --> pdb=" O GLN d 290 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N GLN d 290 " --> pdb=" O ASN d 448 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR d 450 " --> pdb=" O LEU d 288 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS d 330 " --> pdb=" O ILE d 297 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA d 329 " --> pdb=" O CYS d 418 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS d 421 " --> pdb=" O PHE d 382 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE d 382 " --> pdb=" O LYS d 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'd' and resid 271 through 273 removed outlier: 6.505A pdb=" N THR d 450 " --> pdb=" O LEU d 288 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N GLN d 290 " --> pdb=" O ASN d 448 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ASN d 448 " --> pdb=" O GLN d 290 " (cutoff:3.500A) removed outlier: 10.767A pdb=" N VAL d 292 " --> pdb=" O GLU d 446 " (cutoff:3.500A) removed outlier: 9.860A pdb=" N GLU d 446 " --> pdb=" O VAL d 292 " (cutoff:3.500A) removed outlier: 11.496A pdb=" N ILE d 294 " --> pdb=" O LYS d 444 " (cutoff:3.500A) removed outlier: 10.163A pdb=" N LYS d 444 " --> pdb=" O ILE d 294 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'd' and resid 301 through 312 removed outlier: 7.454A pdb=" N ASN d 301 " --> pdb=" O ILE d 323 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ILE d 323 " --> pdb=" O ASN d 301 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N THR d 303 " --> pdb=" O GLY d 321 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLN d 315 " --> pdb=" O ILE d 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'f' and resid 494 through 499 removed outlier: 5.415A pdb=" N VAL g 608 " --> pdb=" O VAL f 36 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL f 38 " --> pdb=" O THR g 606 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N THR g 606 " --> pdb=" O VAL f 38 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N TYR f 40 " --> pdb=" O CYS g 604 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N CYS g 604 " --> pdb=" O TYR f 40 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'f' and resid 45 through 47 Processing sheet with id=AD2, first strand: chain 'f' and resid 53 through 55 Processing sheet with id=AD3, first strand: chain 'f' and resid 66 through 67 removed outlier: 6.746A pdb=" N HIS f 66 " --> pdb=" O SER f 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'f' and resid 91 through 94 Processing sheet with id=AD5, first strand: chain 'f' and resid 169 through 177 Processing sheet with id=AD6, first strand: chain 'f' and resid 202 through 203 removed outlier: 6.330A pdb=" N THR f 202 " --> pdb=" O TYR f 435 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'f' and resid 259 through 261 removed outlier: 3.570A pdb=" N GLY f 451 " --> pdb=" O LEU f 260 " (cutoff:3.500A) removed outlier: 10.120A pdb=" N LYS f 444 " --> pdb=" O ILE f 294 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N ILE f 294 " --> pdb=" O LYS f 444 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N GLU f 446 " --> pdb=" O VAL f 292 " (cutoff:3.500A) removed outlier: 10.762A pdb=" N VAL f 292 " --> pdb=" O GLU f 446 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N ASN f 448 " --> pdb=" O GLN f 290 " (cutoff:3.500A) removed outlier: 10.152A pdb=" N GLN f 290 " --> pdb=" O ASN f 448 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR f 450 " --> pdb=" O LEU f 288 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS f 330 " --> pdb=" O ILE f 297 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA f 329 " --> pdb=" O CYS f 418 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS f 421 " --> pdb=" O PHE f 382 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE f 382 " --> pdb=" O LYS f 421 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'f' and resid 271 through 273 removed outlier: 6.518A pdb=" N THR f 450 " --> pdb=" O LEU f 288 " (cutoff:3.500A) removed outlier: 10.152A pdb=" N GLN f 290 " --> pdb=" O ASN f 448 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N ASN f 448 " --> pdb=" O GLN f 290 " (cutoff:3.500A) removed outlier: 10.762A pdb=" N VAL f 292 " --> pdb=" O GLU f 446 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N GLU f 446 " --> pdb=" O VAL f 292 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N ILE f 294 " --> pdb=" O LYS f 444 " (cutoff:3.500A) removed outlier: 10.120A pdb=" N LYS f 444 " --> pdb=" O ILE f 294 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'f' and resid 301 through 312 removed outlier: 7.085A pdb=" N ASN f 301 " --> pdb=" O ILE f 323 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ILE f 323 " --> pdb=" O ASN f 301 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N THR f 303 " --> pdb=" O GLY f 321 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLN f 315 " --> pdb=" O ILE f 309 " (cutoff:3.500A) 580 hydrogen bonds defined for protein. 1566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.56 Time building geometry restraints manager: 2.57 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: 5213 1.34 - 1.46: 4419 1.46 - 1.58: 7792 1.58 - 1.70: 1 1.70 - 1.82: 144 Bond restraints: 17569 Sorted by residual: bond pdb=" N ARG g 519 " pdb=" CA ARG g 519 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.16e+00 bond pdb=" N GLN e 563 " pdb=" CA GLN e 563 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N ASN b 33 " pdb=" CA ASN b 33 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N ASP d 150 " pdb=" CA ASP d 150 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N GLU f 64 " pdb=" CA GLU f 64 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 ... (remaining 17564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 23060 2.17 - 4.34: 671 4.34 - 6.51: 77 6.51 - 8.68: 11 8.68 - 10.85: 4 Bond angle restraints: 23823 Sorted by residual: angle pdb=" N VAL b 464 " pdb=" CA VAL b 464 " pdb=" C VAL b 464 " ideal model delta sigma weight residual 111.91 107.29 4.62 8.90e-01 1.26e+00 2.69e+01 angle pdb=" CG1 VAL A 110 " pdb=" CB VAL A 110 " pdb=" CG2 VAL A 110 " ideal model delta sigma weight residual 110.80 121.61 -10.81 2.20e+00 2.07e-01 2.42e+01 angle pdb=" CA VAL A 110 " pdb=" CB VAL A 110 " pdb=" CG2 VAL A 110 " ideal model delta sigma weight residual 110.40 117.47 -7.07 1.70e+00 3.46e-01 1.73e+01 angle pdb=" N VAL d 464 " pdb=" CA VAL d 464 " pdb=" C VAL d 464 " ideal model delta sigma weight residual 111.91 108.34 3.57 8.90e-01 1.26e+00 1.61e+01 angle pdb=" CA ASN f 339 " pdb=" CB ASN f 339 " pdb=" CG ASN f 339 " ideal model delta sigma weight residual 112.60 116.35 -3.75 1.00e+00 1.00e+00 1.40e+01 ... (remaining 23818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 11174 17.55 - 35.09: 719 35.09 - 52.64: 225 52.64 - 70.19: 59 70.19 - 87.73: 30 Dihedral angle restraints: 12207 sinusoidal: 6553 harmonic: 5654 Sorted by residual: dihedral pdb=" CB CYS b 126 " pdb=" SG CYS b 126 " pdb=" SG CYS b 196 " pdb=" CB CYS b 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.06 -60.06 1 1.00e+01 1.00e-02 4.81e+01 dihedral pdb=" CB CYS d 126 " pdb=" SG CYS d 126 " pdb=" SG CYS d 196 " pdb=" CB CYS d 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.02 -60.02 1 1.00e+01 1.00e-02 4.80e+01 dihedral pdb=" CB CYS f 126 " pdb=" SG CYS f 126 " pdb=" SG CYS f 196 " pdb=" CB CYS f 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.22 -57.22 1 1.00e+01 1.00e-02 4.40e+01 ... (remaining 12204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.296: 3015 0.296 - 0.592: 2 0.592 - 0.888: 0 0.888 - 1.184: 0 1.184 - 1.480: 1 Chirality restraints: 3018 Sorted by residual: chirality pdb=" CB VAL A 110 " pdb=" CA VAL A 110 " pdb=" CG1 VAL A 110 " pdb=" CG2 VAL A 110 " both_signs ideal model delta sigma weight residual False -2.63 -1.15 -1.48 2.00e-01 2.50e+01 5.48e+01 chirality pdb=" C1 NAG b 601 " pdb=" ND2 ASN b 88 " pdb=" C2 NAG b 601 " pdb=" O5 NAG b 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" C1 NAG f 601 " pdb=" ND2 ASN f 88 " pdb=" C2 NAG f 601 " pdb=" O5 NAG f 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 3015 not shown) Planarity restraints: 2931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 11 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.83e+00 pdb=" N PRO B 12 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 12 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 12 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN d 448 " -0.022 2.00e-02 2.50e+03 2.04e-02 5.22e+00 pdb=" CG ASN d 448 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN d 448 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN d 448 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG Z 1 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN f 448 " 0.021 2.00e-02 2.50e+03 1.96e-02 4.82e+00 pdb=" CG ASN f 448 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN f 448 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN f 448 " -0.023 2.00e-02 2.50e+03 pdb=" C1 NAG r 1 " 0.022 2.00e-02 2.50e+03 ... (remaining 2928 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 220 2.64 - 3.21: 15926 3.21 - 3.77: 24568 3.77 - 4.34: 34944 4.34 - 4.90: 58762 Nonbonded interactions: 134420 Sorted by model distance: nonbonded pdb=" OD2 ASP B 33 " pdb=" O6 NAG l 2 " model vdw 2.079 3.040 nonbonded pdb=" OG SER e 618 " pdb=" OD1 ASP e 620 " model vdw 2.081 3.040 nonbonded pdb=" OG SER A 116 " pdb=" OD2 ASP B 40 " model vdw 2.138 3.040 nonbonded pdb=" OD1 ASP B 31 " pdb=" NH1 ARG B 98 " model vdw 2.150 3.120 nonbonded pdb=" N GLU g 634 " pdb=" OE1 GLU g 634 " model vdw 2.181 3.120 ... (remaining 134415 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 'C' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'h' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'P' selection = chain 'i' } ncs_group { reference = chain 'E' selection = chain 'Q' selection = chain 'j' } ncs_group { reference = (chain 'b' and resid 33 through 607) selection = chain 'd' selection = (chain 'f' and resid 33 through 607) } ncs_group { reference = chain 'c' selection = chain 'e' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 5.730 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: 0.420 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.160 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 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 : 0.004 0.054 17731 Z= 0.171 Angle : 0.960 12.266 24271 Z= 0.485 Chirality : 0.056 1.480 3018 Planarity : 0.005 0.077 2864 Dihedral : 12.984 87.732 8443 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.01 % Favored : 95.93 % Rotamer: Outliers : 0.12 % Allowed : 8.15 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.18), residues: 1918 helix: -0.26 (0.27), residues: 381 sheet: -0.94 (0.22), residues: 500 loop : -1.03 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG e 588 TYR 0.029 0.001 TYR d 173 PHE 0.018 0.002 PHE d 176 TRP 0.029 0.002 TRP b 427 HIS 0.003 0.001 HIS d 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (17569) covalent geometry : angle 0.86639 / 0.47 (23823) SS BOND : bond 0.00292 / 0.19 ( 38) SS BOND : angle 1.52089 / 1.13 ( 76) hydrogen bonds : bond 0.23126 / 15.09 ( 565) hydrogen bonds : angle 8.57655 / 5.82 ( 1566) link_ALPHA1-3 : bond 0.01718 / 0.83 ( 6) link_ALPHA1-3 : angle 3.18425 / 1.77 ( 18) link_ALPHA1-6 : bond 0.01332 / 0.71 ( 5) link_ALPHA1-6 : angle 1.69124 / 0.85 ( 15) link_BETA1-4 : bond 0.00669 / 0.49 ( 46) link_BETA1-4 : angle 3.78218 / 2.53 ( 138) link_NAG-ASN : bond 0.00353 / 0.25 ( 67) link_NAG-ASN : angle 3.24113 / 2.16 ( 201) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 227 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 THR cc_start: 0.9085 (m) cc_final: 0.8771 (p) REVERT: A 73 ASP cc_start: 0.8106 (t0) cc_final: 0.7627 (t0) REVERT: A 87 ARG cc_start: 0.8606 (mpp80) cc_final: 0.8355 (mpp80) REVERT: A 127 THR cc_start: 0.8249 (m) cc_final: 0.7888 (p) REVERT: B 11 LEU cc_start: 0.8228 (tt) cc_final: 0.7704 (tt) REVERT: B 14 THR cc_start: 0.9264 (m) cc_final: 0.8846 (p) REVERT: B 36 ASN cc_start: 0.8390 (m-40) cc_final: 0.8154 (m110) REVERT: B 80 LYS cc_start: 0.8815 (mtpp) cc_final: 0.8582 (tppp) REVERT: c 536 THR cc_start: 0.8788 (p) cc_final: 0.8114 (t) REVERT: c 567 LYS cc_start: 0.7532 (mmtt) cc_final: 0.7039 (tppp) REVERT: c 584 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8396 (mt-10) REVERT: c 622 ILE cc_start: 0.7750 (pt) cc_final: 0.7124 (pt) REVERT: c 632 ASP cc_start: 0.8825 (t70) cc_final: 0.8614 (t0) REVERT: c 654 GLU cc_start: 0.8538 (tp30) cc_final: 0.8005 (tp30) REVERT: c 658 LYS cc_start: 0.8097 (mttt) cc_final: 0.7554 (mttt) REVERT: e 536 THR cc_start: 0.9013 (p) cc_final: 0.8543 (t) REVERT: f 80 ASN cc_start: 0.8992 (t0) cc_final: 0.8618 (p0) REVERT: f 268 LYS cc_start: 0.8313 (mmmt) cc_final: 0.8082 (mtpp) REVERT: g 536 THR cc_start: 0.8995 (p) cc_final: 0.8766 (t) REVERT: g 567 LYS cc_start: 0.7753 (mmtm) cc_final: 0.7254 (mmpt) REVERT: g 620 ASP cc_start: 0.8032 (t0) cc_final: 0.7747 (t0) REVERT: g 624 ASN cc_start: 0.8112 (t0) cc_final: 0.7804 (t160) REVERT: g 657 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7467 (mp0) outliers start: 2 outliers final: 1 residues processed: 229 average time/residue: 0.6561 time to fit residues: 165.8850 Evaluate side-chains 171 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 638 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.0970 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN B 59 ASN c 607 ASN c 624 ASN f 195 ASN f 280 ASN g 543 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.092848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.066601 restraints weight = 39507.943| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 4.22 r_work: 0.2913 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17731 Z= 0.140 Angle : 0.764 16.657 24271 Z= 0.345 Chirality : 0.048 0.415 3018 Planarity : 0.004 0.044 2864 Dihedral : 8.650 74.810 4716 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.35 % Favored : 97.60 % Rotamer: Outliers : 1.73 % Allowed : 9.88 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.18), residues: 1918 helix: -0.13 (0.26), residues: 402 sheet: -0.59 (0.22), residues: 511 loop : -0.69 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG g 542 TYR 0.009 0.001 TYR B 55 PHE 0.013 0.001 PHE d 176 TRP 0.026 0.001 TRP c 631 HIS 0.002 0.001 HIS f 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (17569) covalent geometry : angle 0.67384 / 0.32 (23823) SS BOND : bond 0.00221 / 0.15 ( 38) SS BOND : angle 0.93042 / 0.69 ( 76) hydrogen bonds : bond 0.05393 / 3.51 ( 565) hydrogen bonds : angle 6.08797 / 4.16 ( 1566) link_ALPHA1-3 : bond 0.01069 / 0.46 ( 6) link_ALPHA1-3 : angle 2.75452 / 1.52 ( 18) link_ALPHA1-6 : bond 0.00778 / 0.40 ( 5) link_ALPHA1-6 : angle 1.80577 / 0.93 ( 15) link_BETA1-4 : bond 0.00608 / 0.44 ( 46) link_BETA1-4 : angle 3.38350 / 2.24 ( 138) link_NAG-ASN : bond 0.00442 / 0.29 ( 67) link_NAG-ASN : angle 2.75869 / 1.73 ( 201) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.9152 (mp10) cc_final: 0.8944 (mp10) REVERT: A 69 THR cc_start: 0.9217 (m) cc_final: 0.8875 (p) REVERT: A 73 ASP cc_start: 0.8130 (t0) cc_final: 0.6768 (t0) REVERT: A 76 LYS cc_start: 0.8929 (mtmm) cc_final: 0.8034 (mtmm) REVERT: A 87 ARG cc_start: 0.7987 (mpp80) cc_final: 0.7617 (mpp80) REVERT: A 127 THR cc_start: 0.7817 (m) cc_final: 0.7348 (p) REVERT: B 36 ASN cc_start: 0.8388 (m-40) cc_final: 0.7907 (m110) REVERT: B 76 ASP cc_start: 0.8586 (t70) cc_final: 0.8362 (p0) REVERT: B 80 LYS cc_start: 0.8948 (mtpp) cc_final: 0.8731 (tppp) REVERT: c 536 THR cc_start: 0.8930 (p) cc_final: 0.8475 (t) REVERT: c 567 LYS cc_start: 0.7407 (mmtt) cc_final: 0.6790 (tppp) REVERT: c 584 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8344 (mt-10) REVERT: c 626 MET cc_start: 0.6837 (ttm) cc_final: 0.6479 (ttm) REVERT: c 632 ASP cc_start: 0.8839 (t70) cc_final: 0.8632 (t0) REVERT: c 654 GLU cc_start: 0.8315 (tp30) cc_final: 0.8071 (tp30) REVERT: c 658 LYS cc_start: 0.8090 (mttt) cc_final: 0.7732 (mttt) REVERT: e 536 THR cc_start: 0.9017 (p) cc_final: 0.8515 (t) REVERT: e 567 LYS cc_start: 0.8631 (tppt) cc_final: 0.7855 (mppt) REVERT: f 268 LYS cc_start: 0.8291 (mmmt) cc_final: 0.7881 (mtpp) REVERT: g 536 THR cc_start: 0.9045 (p) cc_final: 0.8823 (t) REVERT: g 567 LYS cc_start: 0.7821 (mmtm) cc_final: 0.7131 (mmpt) outliers start: 30 outliers final: 16 residues processed: 199 average time/residue: 0.6528 time to fit residues: 144.2032 Evaluate side-chains 171 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 496 VAL Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain e residue 648 GLU Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 452 LEU Chi-restraints excluded: chain g residue 639 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 20 optimal weight: 5.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 80 ASN b 330 HIS c 607 ASN ** e 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 607 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.091623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.065202 restraints weight = 39742.606| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 4.23 r_work: 0.2884 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17731 Z= 0.146 Angle : 0.729 16.881 24271 Z= 0.327 Chirality : 0.047 0.341 3018 Planarity : 0.004 0.040 2864 Dihedral : 8.359 71.801 4714 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.29 % Favored : 97.65 % Rotamer: Outliers : 2.25 % Allowed : 10.57 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.18), residues: 1918 helix: -0.20 (0.26), residues: 420 sheet: -0.40 (0.22), residues: 497 loop : -0.65 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 24 TYR 0.009 0.001 TYR A 103 PHE 0.012 0.001 PHE f 383 TRP 0.016 0.001 TRP c 631 HIS 0.003 0.001 HIS f 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (17569) covalent geometry : angle 0.64163 / 0.31 (23823) SS BOND : bond 0.00269 / 0.19 ( 38) SS BOND : angle 0.87725 / 0.64 ( 76) hydrogen bonds : bond 0.04659 / 3.04 ( 565) hydrogen bonds : angle 5.53272 / 3.81 ( 1566) link_ALPHA1-3 : bond 0.01136 / 0.49 ( 6) link_ALPHA1-3 : angle 2.64557 / 1.46 ( 18) link_ALPHA1-6 : bond 0.00751 / 0.38 ( 5) link_ALPHA1-6 : angle 1.76331 / 0.90 ( 15) link_BETA1-4 : bond 0.00607 / 0.44 ( 46) link_BETA1-4 : angle 3.13530 / 2.08 ( 138) link_NAG-ASN : bond 0.00351 / 0.25 ( 67) link_NAG-ASN : angle 2.72186 / 1.68 ( 201) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.9197 (mp10) cc_final: 0.8891 (mp10) REVERT: A 69 THR cc_start: 0.9244 (m) cc_final: 0.8882 (p) REVERT: A 73 ASP cc_start: 0.8213 (t0) cc_final: 0.7595 (t0) REVERT: A 87 ARG cc_start: 0.8017 (mpp80) cc_final: 0.7711 (mpp80) REVERT: A 127 THR cc_start: 0.7860 (m) cc_final: 0.7405 (p) REVERT: B 36 ASN cc_start: 0.8410 (m-40) cc_final: 0.8171 (m110) REVERT: B 76 ASP cc_start: 0.8660 (t70) cc_final: 0.8426 (p0) REVERT: B 80 LYS cc_start: 0.8929 (mtpp) cc_final: 0.8673 (tppp) REVERT: b 500 ARG cc_start: 0.7716 (ptp-170) cc_final: 0.7212 (ttm-80) REVERT: c 536 THR cc_start: 0.8907 (p) cc_final: 0.8453 (t) REVERT: c 584 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8389 (mt-10) REVERT: c 626 MET cc_start: 0.7067 (ttm) cc_final: 0.6764 (ttm) REVERT: c 654 GLU cc_start: 0.8282 (tp30) cc_final: 0.8015 (tp30) REVERT: c 658 LYS cc_start: 0.8055 (mttt) cc_final: 0.7693 (mttt) REVERT: e 536 THR cc_start: 0.9131 (p) cc_final: 0.8752 (t) REVERT: f 268 LYS cc_start: 0.8354 (mmmt) cc_final: 0.7943 (mtpp) REVERT: g 520 ARG cc_start: 0.8494 (mmt-90) cc_final: 0.8224 (mmm-85) REVERT: g 530 MET cc_start: 0.8651 (mtp) cc_final: 0.8344 (mtp) REVERT: g 536 THR cc_start: 0.9043 (p) cc_final: 0.8830 (t) REVERT: g 567 LYS cc_start: 0.7846 (mmtm) cc_final: 0.7104 (mmpt) outliers start: 39 outliers final: 17 residues processed: 192 average time/residue: 0.6508 time to fit residues: 138.8367 Evaluate side-chains 168 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 162 THR Chi-restraints excluded: chain b residue 496 VAL Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 452 LEU Chi-restraints excluded: chain g residue 638 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 41 optimal weight: 0.9980 chunk 151 optimal weight: 0.0010 chunk 184 optimal weight: 0.8980 chunk 140 optimal weight: 0.0000 chunk 34 optimal weight: 5.9990 chunk 171 optimal weight: 0.0980 chunk 6 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 143 optimal weight: 0.6980 chunk 186 optimal weight: 4.9990 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 80 ASN c 607 ASN d 330 HIS e 607 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.093028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.066759 restraints weight = 39564.264| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 4.23 r_work: 0.2920 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17731 Z= 0.107 Angle : 0.680 16.784 24271 Z= 0.303 Chirality : 0.046 0.341 3018 Planarity : 0.003 0.042 2864 Dihedral : 8.104 69.901 4714 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.19 % Favored : 97.76 % Rotamer: Outliers : 1.91 % Allowed : 11.90 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.19), residues: 1918 helix: 0.33 (0.27), residues: 390 sheet: -0.25 (0.22), residues: 505 loop : -0.59 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 24 TYR 0.012 0.001 TYR A 60 PHE 0.008 0.001 PHE f 210 TRP 0.011 0.001 TRP d 338 HIS 0.002 0.000 HIS b 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (17569) covalent geometry : angle 0.59692 / 0.28 (23823) SS BOND : bond 0.00178 / 0.12 ( 38) SS BOND : angle 0.69582 / 0.49 ( 76) hydrogen bonds : bond 0.03858 / 2.53 ( 565) hydrogen bonds : angle 5.24496 / 3.62 ( 1566) link_ALPHA1-3 : bond 0.01152 / 0.50 ( 6) link_ALPHA1-3 : angle 2.68510 / 1.48 ( 18) link_ALPHA1-6 : bond 0.00844 / 0.43 ( 5) link_ALPHA1-6 : angle 1.63017 / 0.84 ( 15) link_BETA1-4 : bond 0.00617 / 0.44 ( 46) link_BETA1-4 : angle 2.98774 / 1.98 ( 138) link_NAG-ASN : bond 0.00372 / 0.26 ( 67) link_NAG-ASN : angle 2.53007 / 1.56 ( 201) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.9255 (mp10) cc_final: 0.8934 (mp10) REVERT: A 69 THR cc_start: 0.9237 (m) cc_final: 0.8842 (p) REVERT: A 73 ASP cc_start: 0.8223 (t0) cc_final: 0.7625 (t0) REVERT: A 87 ARG cc_start: 0.8021 (mpp80) cc_final: 0.7700 (mpp80) REVERT: A 127 THR cc_start: 0.7832 (m) cc_final: 0.7367 (p) REVERT: B 36 ASN cc_start: 0.8241 (m-40) cc_final: 0.8011 (m-40) REVERT: B 39 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8816 (tp) REVERT: B 60 ARG cc_start: 0.8312 (mtp-110) cc_final: 0.7918 (mtp85) REVERT: B 76 ASP cc_start: 0.8686 (t70) cc_final: 0.8477 (p0) REVERT: c 536 THR cc_start: 0.8876 (p) cc_final: 0.8311 (t) REVERT: c 544 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8690 (mm) REVERT: c 584 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8501 (mt-10) REVERT: c 626 MET cc_start: 0.6774 (ttm) cc_final: 0.6520 (ttm) REVERT: c 658 LYS cc_start: 0.8034 (mttt) cc_final: 0.7773 (mtmt) REVERT: e 536 THR cc_start: 0.9143 (p) cc_final: 0.8816 (t) REVERT: e 567 LYS cc_start: 0.8657 (tppt) cc_final: 0.7910 (mppt) REVERT: f 268 LYS cc_start: 0.8348 (mmmt) cc_final: 0.7911 (mtpp) REVERT: g 567 LYS cc_start: 0.7845 (mmtm) cc_final: 0.7151 (mppt) outliers start: 33 outliers final: 16 residues processed: 190 average time/residue: 0.6027 time to fit residues: 127.5972 Evaluate side-chains 168 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 496 VAL Chi-restraints excluded: chain c residue 544 LEU Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 452 LEU Chi-restraints excluded: chain g residue 638 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 3 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 607 ASN f 330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.090863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.064728 restraints weight = 39303.100| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 4.16 r_work: 0.2874 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17731 Z= 0.159 Angle : 0.698 16.918 24271 Z= 0.312 Chirality : 0.046 0.339 3018 Planarity : 0.003 0.041 2864 Dihedral : 8.006 69.628 4714 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.24 % Favored : 97.71 % Rotamer: Outliers : 2.72 % Allowed : 11.79 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.19), residues: 1918 helix: 0.33 (0.27), residues: 390 sheet: -0.19 (0.23), residues: 499 loop : -0.58 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 24 TYR 0.015 0.001 TYR g 638 PHE 0.013 0.001 PHE b 383 TRP 0.011 0.001 TRP d 338 HIS 0.004 0.001 HIS f 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (17569) covalent geometry : angle 0.60938 / 0.29 (23823) SS BOND : bond 0.00258 / 0.17 ( 38) SS BOND : angle 0.81217 / 0.57 ( 76) hydrogen bonds : bond 0.04101 / 2.70 ( 565) hydrogen bonds : angle 5.16948 / 3.56 ( 1566) link_ALPHA1-3 : bond 0.01102 / 0.48 ( 6) link_ALPHA1-3 : angle 2.59094 / 1.43 ( 18) link_ALPHA1-6 : bond 0.00824 / 0.42 ( 5) link_ALPHA1-6 : angle 1.58907 / 0.82 ( 15) link_BETA1-4 : bond 0.00598 / 0.43 ( 46) link_BETA1-4 : angle 2.94174 / 1.96 ( 138) link_NAG-ASN : bond 0.00338 / 0.25 ( 67) link_NAG-ASN : angle 2.80978 / 1.73 ( 201) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.9289 (mp10) cc_final: 0.8961 (mp10) REVERT: A 69 THR cc_start: 0.9221 (m) cc_final: 0.8806 (p) REVERT: A 73 ASP cc_start: 0.8284 (t0) cc_final: 0.7688 (t0) REVERT: A 87 ARG cc_start: 0.7995 (mpp80) cc_final: 0.7769 (mpp80) REVERT: A 127 THR cc_start: 0.7897 (m) cc_final: 0.7441 (p) REVERT: B 36 ASN cc_start: 0.8263 (m-40) cc_final: 0.7875 (m110) REVERT: B 60 ARG cc_start: 0.8355 (mtp-110) cc_final: 0.8153 (mtp85) REVERT: B 85 GLU cc_start: 0.6483 (mp0) cc_final: 0.6153 (mp0) REVERT: c 536 THR cc_start: 0.8880 (p) cc_final: 0.8351 (t) REVERT: c 584 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8393 (mt-10) REVERT: c 621 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7086 (pp20) REVERT: c 626 MET cc_start: 0.6747 (ttm) cc_final: 0.6424 (ttm) REVERT: c 658 LYS cc_start: 0.8107 (mttt) cc_final: 0.7839 (mttt) REVERT: e 536 THR cc_start: 0.9134 (p) cc_final: 0.8834 (t) REVERT: e 567 LYS cc_start: 0.8737 (tppt) cc_final: 0.8028 (mppt) REVERT: e 657 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6922 (tm-30) REVERT: f 268 LYS cc_start: 0.8417 (mmmt) cc_final: 0.7864 (mtpp) REVERT: g 530 MET cc_start: 0.8390 (mtp) cc_final: 0.8188 (mtp) REVERT: g 567 LYS cc_start: 0.7857 (mmtm) cc_final: 0.7179 (mmpt) outliers start: 47 outliers final: 24 residues processed: 193 average time/residue: 0.6121 time to fit residues: 131.6653 Evaluate side-chains 176 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 162 THR Chi-restraints excluded: chain b residue 496 VAL Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 621 GLU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain e residue 544 LEU Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 452 LEU Chi-restraints excluded: chain g residue 639 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 51 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN b 80 ASN d 187 ASN e 607 ASN f 80 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.089755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.062866 restraints weight = 39533.950| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 4.27 r_work: 0.2832 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 17731 Z= 0.209 Angle : 0.734 17.074 24271 Z= 0.330 Chirality : 0.047 0.343 3018 Planarity : 0.004 0.045 2864 Dihedral : 8.057 69.988 4714 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.29 % Rotamer: Outliers : 2.72 % Allowed : 12.31 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.19), residues: 1918 helix: 0.31 (0.27), residues: 390 sheet: -0.19 (0.22), residues: 498 loop : -0.65 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 24 TYR 0.021 0.001 TYR g 638 PHE 0.017 0.002 PHE b 383 TRP 0.011 0.001 TRP d 338 HIS 0.005 0.001 HIS f 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 (17569) covalent geometry : angle 0.64845 / 0.31 (23823) SS BOND : bond 0.00318 / 0.21 ( 38) SS BOND : angle 1.00123 / 0.70 ( 76) hydrogen bonds : bond 0.04316 / 2.82 ( 565) hydrogen bonds : angle 5.18537 / 3.56 ( 1566) link_ALPHA1-3 : bond 0.01059 / 0.48 ( 6) link_ALPHA1-3 : angle 2.56389 / 1.42 ( 18) link_ALPHA1-6 : bond 0.00815 / 0.41 ( 5) link_ALPHA1-6 : angle 1.58137 / 0.81 ( 15) link_BETA1-4 : bond 0.00587 / 0.42 ( 46) link_BETA1-4 : angle 2.92626 / 1.95 ( 138) link_NAG-ASN : bond 0.00345 / 0.25 ( 67) link_NAG-ASN : angle 2.86180 / 1.73 ( 201) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.9316 (mp10) cc_final: 0.8993 (mp10) REVERT: A 28 ILE cc_start: 0.8557 (mm) cc_final: 0.8270 (mt) REVERT: A 69 THR cc_start: 0.9230 (m) cc_final: 0.8813 (p) REVERT: A 73 ASP cc_start: 0.8339 (t0) cc_final: 0.7697 (t0) REVERT: A 87 ARG cc_start: 0.7971 (mpp80) cc_final: 0.7688 (mpp80) REVERT: A 127 THR cc_start: 0.7883 (m) cc_final: 0.7414 (p) REVERT: B 60 ARG cc_start: 0.8474 (mtp-110) cc_final: 0.8045 (mtp85) REVERT: B 85 GLU cc_start: 0.6423 (mp0) cc_final: 0.6215 (mp0) REVERT: c 536 THR cc_start: 0.8925 (p) cc_final: 0.8406 (t) REVERT: c 584 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8374 (mt-10) REVERT: c 621 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7026 (pp20) REVERT: c 658 LYS cc_start: 0.8119 (mttt) cc_final: 0.7822 (mttt) REVERT: e 536 THR cc_start: 0.9102 (p) cc_final: 0.8822 (t) REVERT: e 567 LYS cc_start: 0.8730 (tppt) cc_final: 0.8008 (mppt) REVERT: f 268 LYS cc_start: 0.8515 (mmmt) cc_final: 0.7935 (mtpp) REVERT: g 530 MET cc_start: 0.8318 (mtp) cc_final: 0.8039 (mtp) REVERT: g 567 LYS cc_start: 0.7828 (mmtm) cc_final: 0.7119 (mmpt) REVERT: g 568 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8380 (tm) REVERT: g 633 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8746 (ptpp) outliers start: 47 outliers final: 29 residues processed: 189 average time/residue: 0.6219 time to fit residues: 130.3359 Evaluate side-chains 179 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 162 THR Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain b residue 496 VAL Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 621 GLU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 378 CYS Chi-restraints excluded: chain g residue 568 LEU Chi-restraints excluded: chain g residue 633 LYS Chi-restraints excluded: chain g residue 638 TYR Chi-restraints excluded: chain g residue 639 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 133 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 152 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 154 optimal weight: 0.0020 chunk 188 optimal weight: 4.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 607 ASN e 607 ASN f 80 ASN ** g 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.090980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.064556 restraints weight = 39383.803| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 4.25 r_work: 0.2871 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17731 Z= 0.117 Angle : 0.684 16.863 24271 Z= 0.307 Chirality : 0.045 0.331 3018 Planarity : 0.003 0.048 2864 Dihedral : 7.843 68.595 4714 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.20 % Allowed : 13.00 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.19), residues: 1918 helix: 0.61 (0.28), residues: 372 sheet: -0.15 (0.22), residues: 507 loop : -0.55 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 24 TYR 0.022 0.001 TYR g 638 PHE 0.010 0.001 PHE f 383 TRP 0.013 0.001 TRP d 338 HIS 0.002 0.001 HIS b 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (17569) covalent geometry : angle 0.60007 / 0.29 (23823) SS BOND : bond 0.00244 / 0.14 ( 38) SS BOND : angle 0.81139 / 0.56 ( 76) hydrogen bonds : bond 0.03815 / 2.50 ( 565) hydrogen bonds : angle 5.01359 / 3.46 ( 1566) link_ALPHA1-3 : bond 0.01029 / 0.46 ( 6) link_ALPHA1-3 : angle 2.53080 / 1.40 ( 18) link_ALPHA1-6 : bond 0.00855 / 0.44 ( 5) link_ALPHA1-6 : angle 1.57012 / 0.80 ( 15) link_BETA1-4 : bond 0.00592 / 0.42 ( 46) link_BETA1-4 : angle 2.84893 / 1.90 ( 138) link_NAG-ASN : bond 0.00316 / 0.23 ( 67) link_NAG-ASN : angle 2.70435 / 1.63 ( 201) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.9335 (mp10) cc_final: 0.9023 (mp10) REVERT: A 28 ILE cc_start: 0.8539 (mm) cc_final: 0.8288 (mt) REVERT: A 69 THR cc_start: 0.9210 (m) cc_final: 0.8789 (p) REVERT: A 73 ASP cc_start: 0.8315 (t0) cc_final: 0.7692 (t0) REVERT: A 87 ARG cc_start: 0.8001 (mpp80) cc_final: 0.7722 (mpp80) REVERT: A 127 THR cc_start: 0.7864 (m) cc_final: 0.7369 (p) REVERT: B 60 ARG cc_start: 0.8473 (mtp-110) cc_final: 0.8051 (mtp85) REVERT: B 85 GLU cc_start: 0.6421 (mp0) cc_final: 0.6170 (mp0) REVERT: B 98 ARG cc_start: 0.8792 (mmm160) cc_final: 0.8516 (mmm-85) REVERT: c 536 THR cc_start: 0.8845 (p) cc_final: 0.8310 (t) REVERT: c 544 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8796 (mm) REVERT: c 584 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8452 (mt-10) REVERT: c 621 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7215 (pp20) REVERT: c 626 MET cc_start: 0.6942 (mtp) cc_final: 0.6316 (ttm) REVERT: c 658 LYS cc_start: 0.8077 (mttt) cc_final: 0.7795 (mtmt) REVERT: e 536 THR cc_start: 0.9094 (p) cc_final: 0.8818 (t) REVERT: e 567 LYS cc_start: 0.8730 (tppt) cc_final: 0.8020 (mppt) REVERT: e 657 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6919 (tm-30) REVERT: f 268 LYS cc_start: 0.8523 (mmmt) cc_final: 0.7936 (mtpp) REVERT: g 567 LYS cc_start: 0.7852 (mmtm) cc_final: 0.7132 (mmpt) outliers start: 38 outliers final: 25 residues processed: 186 average time/residue: 0.6210 time to fit residues: 127.9587 Evaluate side-chains 174 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 162 THR Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain b residue 496 VAL Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 544 LEU Chi-restraints excluded: chain c residue 621 GLU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 161 MET Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 452 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 12 optimal weight: 0.2980 chunk 95 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 186 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 607 ASN d 80 ASN e 607 ASN f 80 ASN ** g 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.091099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.064681 restraints weight = 39539.740| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 4.25 r_work: 0.2874 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17731 Z= 0.123 Angle : 0.689 16.783 24271 Z= 0.309 Chirality : 0.045 0.322 3018 Planarity : 0.003 0.052 2864 Dihedral : 7.745 68.080 4714 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.02 % Allowed : 13.52 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.19), residues: 1918 helix: 0.67 (0.28), residues: 372 sheet: -0.11 (0.22), residues: 506 loop : -0.52 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 24 TYR 0.008 0.001 TYR A 103 PHE 0.009 0.001 PHE f 317 TRP 0.012 0.001 TRP d 338 HIS 0.002 0.001 HIS f 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (17569) covalent geometry : angle 0.60760 / 0.29 (23823) SS BOND : bond 0.00201 / 0.13 ( 38) SS BOND : angle 0.76164 / 0.54 ( 76) hydrogen bonds : bond 0.03727 / 2.44 ( 565) hydrogen bonds : angle 4.98373 / 3.44 ( 1566) link_ALPHA1-3 : bond 0.01017 / 0.45 ( 6) link_ALPHA1-3 : angle 2.47313 / 1.36 ( 18) link_ALPHA1-6 : bond 0.00851 / 0.44 ( 5) link_ALPHA1-6 : angle 1.57131 / 0.81 ( 15) link_BETA1-4 : bond 0.00592 / 0.42 ( 46) link_BETA1-4 : angle 2.81044 / 1.87 ( 138) link_NAG-ASN : bond 0.00320 / 0.23 ( 67) link_NAG-ASN : angle 2.66775 / 1.60 ( 201) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.9333 (mp10) cc_final: 0.9019 (mp10) REVERT: A 28 ILE cc_start: 0.8577 (mm) cc_final: 0.8350 (mt) REVERT: A 69 THR cc_start: 0.9209 (m) cc_final: 0.8781 (p) REVERT: A 73 ASP cc_start: 0.8336 (t0) cc_final: 0.7717 (t0) REVERT: A 87 ARG cc_start: 0.8014 (mpp80) cc_final: 0.7726 (mpp80) REVERT: A 127 THR cc_start: 0.7861 (m) cc_final: 0.7357 (p) REVERT: B 36 ASN cc_start: 0.8343 (m110) cc_final: 0.8033 (t0) REVERT: B 85 GLU cc_start: 0.6422 (mp0) cc_final: 0.6193 (mp0) REVERT: B 98 ARG cc_start: 0.8791 (mmm160) cc_final: 0.8529 (mmm-85) REVERT: c 536 THR cc_start: 0.8855 (p) cc_final: 0.8315 (t) REVERT: c 544 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8799 (mm) REVERT: c 584 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8517 (mt-10) REVERT: c 621 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7249 (pp20) REVERT: c 626 MET cc_start: 0.7068 (mtp) cc_final: 0.6522 (ttm) REVERT: c 658 LYS cc_start: 0.8127 (mttt) cc_final: 0.7848 (mtmt) REVERT: e 536 THR cc_start: 0.9104 (p) cc_final: 0.8819 (t) REVERT: e 567 LYS cc_start: 0.8703 (tppt) cc_final: 0.7981 (mppt) REVERT: e 657 GLU cc_start: 0.7198 (tm-30) cc_final: 0.6886 (tm-30) REVERT: f 268 LYS cc_start: 0.8546 (mmmt) cc_final: 0.7994 (mtpp) REVERT: g 567 LYS cc_start: 0.7847 (mmtm) cc_final: 0.7122 (mmpt) REVERT: g 588 ARG cc_start: 0.9157 (ttp80) cc_final: 0.8952 (ttp-170) REVERT: g 617 LYS cc_start: 0.7106 (mmmm) cc_final: 0.6807 (tptp) outliers start: 35 outliers final: 23 residues processed: 182 average time/residue: 0.6377 time to fit residues: 128.3070 Evaluate side-chains 171 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 162 THR Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain b residue 496 VAL Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 544 LEU Chi-restraints excluded: chain c residue 621 GLU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 161 MET Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 378 CYS Chi-restraints excluded: chain f residue 452 LEU Chi-restraints excluded: chain g residue 638 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 111 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 607 ASN e 651 ASN f 80 ASN ** g 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 616 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.090756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.064628 restraints weight = 39643.814| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 4.21 r_work: 0.2867 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17731 Z= 0.137 Angle : 0.693 16.712 24271 Z= 0.312 Chirality : 0.046 0.312 3018 Planarity : 0.004 0.056 2864 Dihedral : 7.684 67.595 4714 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.02 % Allowed : 13.69 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.19), residues: 1918 helix: 0.66 (0.28), residues: 372 sheet: -0.08 (0.22), residues: 506 loop : -0.53 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 24 TYR 0.010 0.001 TYR e 643 PHE 0.011 0.001 PHE b 383 TRP 0.011 0.001 TRP e 631 HIS 0.003 0.001 HIS f 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (17569) covalent geometry : angle 0.61421 / 0.29 (23823) SS BOND : bond 0.00214 / 0.14 ( 38) SS BOND : angle 0.95739 / 0.72 ( 76) hydrogen bonds : bond 0.03749 / 2.45 ( 565) hydrogen bonds : angle 5.00065 / 3.45 ( 1566) link_ALPHA1-3 : bond 0.00996 / 0.44 ( 6) link_ALPHA1-3 : angle 2.40130 / 1.32 ( 18) link_ALPHA1-6 : bond 0.00827 / 0.42 ( 5) link_ALPHA1-6 : angle 1.58866 / 0.83 ( 15) link_BETA1-4 : bond 0.00590 / 0.42 ( 46) link_BETA1-4 : angle 2.78192 / 1.86 ( 138) link_NAG-ASN : bond 0.00318 / 0.23 ( 67) link_NAG-ASN : angle 2.64281 / 1.59 ( 201) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.9328 (mp10) cc_final: 0.9001 (mp10) REVERT: A 28 ILE cc_start: 0.8582 (mm) cc_final: 0.8370 (mt) REVERT: A 69 THR cc_start: 0.9205 (m) cc_final: 0.8770 (p) REVERT: A 73 ASP cc_start: 0.8351 (t0) cc_final: 0.7727 (t0) REVERT: A 127 THR cc_start: 0.7871 (m) cc_final: 0.7363 (p) REVERT: B 36 ASN cc_start: 0.8322 (m110) cc_final: 0.8069 (t0) REVERT: B 48 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7687 (tp-100) REVERT: B 85 GLU cc_start: 0.6432 (mp0) cc_final: 0.6176 (mp0) REVERT: B 98 ARG cc_start: 0.8782 (mmm160) cc_final: 0.8521 (mmm-85) REVERT: c 536 THR cc_start: 0.8854 (p) cc_final: 0.8316 (t) REVERT: c 544 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8830 (mm) REVERT: c 584 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8527 (mt-10) REVERT: c 621 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7183 (pp20) REVERT: c 626 MET cc_start: 0.7257 (mtp) cc_final: 0.6625 (ttm) REVERT: c 658 LYS cc_start: 0.8138 (mttt) cc_final: 0.7866 (mtmt) REVERT: e 536 THR cc_start: 0.9089 (p) cc_final: 0.8802 (t) REVERT: e 567 LYS cc_start: 0.8710 (tppt) cc_final: 0.7994 (mppt) REVERT: e 588 ARG cc_start: 0.8931 (ttp80) cc_final: 0.8727 (ttp80) REVERT: e 639 THR cc_start: 0.8429 (m) cc_final: 0.8215 (p) REVERT: e 657 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6953 (tm-30) REVERT: f 268 LYS cc_start: 0.8567 (mmmt) cc_final: 0.7991 (mtpp) REVERT: g 567 LYS cc_start: 0.7840 (mmtm) cc_final: 0.7119 (mppt) REVERT: g 617 LYS cc_start: 0.7180 (mmmm) cc_final: 0.6775 (tptp) outliers start: 35 outliers final: 23 residues processed: 187 average time/residue: 0.6204 time to fit residues: 128.7973 Evaluate side-chains 173 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 162 THR Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain b residue 496 VAL Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 544 LEU Chi-restraints excluded: chain c residue 621 GLU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 378 CYS Chi-restraints excluded: chain f residue 452 LEU Chi-restraints excluded: chain g residue 638 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 425 ASN c 607 ASN ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 607 ASN f 80 ASN ** g 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 624 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.090267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.064064 restraints weight = 39479.836| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 4.20 r_work: 0.2856 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17731 Z= 0.158 Angle : 0.708 16.701 24271 Z= 0.320 Chirality : 0.046 0.305 3018 Planarity : 0.004 0.084 2864 Dihedral : 7.681 67.667 4714 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.68 % Allowed : 14.10 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.19), residues: 1918 helix: 0.67 (0.28), residues: 372 sheet: 0.11 (0.23), residues: 477 loop : -0.56 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 24 TYR 0.020 0.001 TYR e 643 PHE 0.013 0.001 PHE b 383 TRP 0.013 0.001 TRP g 631 HIS 0.003 0.001 HIS f 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (17569) covalent geometry : angle 0.63147 / 0.30 (23823) SS BOND : bond 0.00240 / 0.16 ( 38) SS BOND : angle 1.03024 / 0.80 ( 76) hydrogen bonds : bond 0.03875 / 2.53 ( 565) hydrogen bonds : angle 5.04419 / 3.48 ( 1566) link_ALPHA1-3 : bond 0.00953 / 0.44 ( 6) link_ALPHA1-3 : angle 2.35570 / 1.30 ( 18) link_ALPHA1-6 : bond 0.00765 / 0.39 ( 5) link_ALPHA1-6 : angle 1.59597 / 0.84 ( 15) link_BETA1-4 : bond 0.00583 / 0.41 ( 46) link_BETA1-4 : angle 2.76770 / 1.85 ( 138) link_NAG-ASN : bond 0.00320 / 0.23 ( 67) link_NAG-ASN : angle 2.64193 / 1.58 ( 201) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.9342 (mp10) cc_final: 0.9016 (mp10) REVERT: A 28 ILE cc_start: 0.8564 (mm) cc_final: 0.8354 (mt) REVERT: A 69 THR cc_start: 0.9208 (m) cc_final: 0.8760 (p) REVERT: A 73 ASP cc_start: 0.8358 (t0) cc_final: 0.7713 (t0) REVERT: A 87 ARG cc_start: 0.8121 (mpp80) cc_final: 0.7784 (mpp80) REVERT: A 127 THR cc_start: 0.7867 (m) cc_final: 0.7350 (p) REVERT: B 36 ASN cc_start: 0.8295 (m110) cc_final: 0.8021 (t0) REVERT: B 48 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7770 (tp-100) REVERT: B 60 ARG cc_start: 0.8231 (mtp-110) cc_final: 0.7587 (mtp85) REVERT: B 66 ASP cc_start: 0.8857 (t0) cc_final: 0.8415 (t0) REVERT: B 85 GLU cc_start: 0.6458 (mp0) cc_final: 0.6158 (mp0) REVERT: B 98 ARG cc_start: 0.8810 (mmm160) cc_final: 0.8512 (mmm-85) REVERT: c 536 THR cc_start: 0.8853 (p) cc_final: 0.8319 (t) REVERT: c 544 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8856 (mm) REVERT: c 584 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8391 (mt-10) REVERT: c 621 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7270 (pp20) REVERT: c 626 MET cc_start: 0.7202 (mtp) cc_final: 0.6634 (ttm) REVERT: c 658 LYS cc_start: 0.8138 (mttt) cc_final: 0.7881 (mtmt) REVERT: d 46 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.8080 (ptp-110) REVERT: e 536 THR cc_start: 0.9061 (p) cc_final: 0.8772 (t) REVERT: e 567 LYS cc_start: 0.8705 (tppt) cc_final: 0.7973 (mppt) REVERT: e 639 THR cc_start: 0.8487 (m) cc_final: 0.8248 (p) REVERT: f 268 LYS cc_start: 0.8578 (mmmt) cc_final: 0.7977 (mtpp) REVERT: g 567 LYS cc_start: 0.7855 (mmtm) cc_final: 0.7130 (mmpt) REVERT: g 617 LYS cc_start: 0.7233 (mmmm) cc_final: 0.6918 (tptp) outliers start: 29 outliers final: 23 residues processed: 171 average time/residue: 0.6451 time to fit residues: 121.9477 Evaluate side-chains 169 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 162 THR Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain b residue 496 VAL Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 544 LEU Chi-restraints excluded: chain c residue 621 GLU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 123 THR Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 378 CYS Chi-restraints excluded: chain f residue 452 LEU Chi-restraints excluded: chain g residue 638 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 607 ASN ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 607 ASN f 80 ASN ** g 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 616 ASN g 624 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.090800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.064659 restraints weight = 39651.651| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 4.21 r_work: 0.2868 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17731 Z= 0.134 Angle : 0.697 16.604 24271 Z= 0.313 Chirality : 0.045 0.296 3018 Planarity : 0.003 0.055 2864 Dihedral : 7.601 66.855 4714 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.62 % Allowed : 14.27 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.19), residues: 1918 helix: 0.70 (0.28), residues: 372 sheet: 0.15 (0.23), residues: 477 loop : -0.52 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 24 TYR 0.009 0.001 TYR A 103 PHE 0.010 0.001 PHE b 383 TRP 0.012 0.001 TRP d 338 HIS 0.003 0.001 HIS b 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (17569) covalent geometry : angle 0.62213 / 0.30 (23823) SS BOND : bond 0.00212 / 0.14 ( 38) SS BOND : angle 0.90928 / 0.69 ( 76) hydrogen bonds : bond 0.03718 / 2.43 ( 565) hydrogen bonds : angle 4.98831 / 3.45 ( 1566) link_ALPHA1-3 : bond 0.00931 / 0.43 ( 6) link_ALPHA1-3 : angle 2.32081 / 1.27 ( 18) link_ALPHA1-6 : bond 0.00781 / 0.40 ( 5) link_ALPHA1-6 : angle 1.61572 / 0.85 ( 15) link_BETA1-4 : bond 0.00582 / 0.41 ( 46) link_BETA1-4 : angle 2.73388 / 1.83 ( 138) link_NAG-ASN : bond 0.00316 / 0.23 ( 67) link_NAG-ASN : angle 2.59315 / 1.55 ( 201) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4779.47 seconds wall clock time: 82 minutes 38.62 seconds (4958.62 seconds total)