Starting phenix.real_space_refine on Mon May 4 03:30:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nvz_49869/05_2026/9nvz_49869.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nvz_49869/05_2026/9nvz_49869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nvz_49869/05_2026/9nvz_49869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nvz_49869/05_2026/9nvz_49869.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nvz_49869/05_2026/9nvz_49869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nvz_49869/05_2026/9nvz_49869.map" } resolution = 3.0 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= 0.001 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 108 5.16 5 C 10786 2.51 5 N 2850 2.21 5 O 3550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17294 Number of models: 1 Model: "" Number of chains: 56 Chain: "H" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1067 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "b" Number of atoms: 3530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3530 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: 3530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3530 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: 3530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3530 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: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 3.93, per 1000 atoms: 0.23 Number of scatterers: 17294 At special positions: 0 Unit cell: (130.31, 129.48, 157.7, 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 108 16.00 O 3550 8.00 N 2850 7.00 C 10786 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 98 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS b 54 " - pdb=" SG CYS b 74 " distance=2.04 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS d 228 " - pdb=" SG CYS d 239 " distance=2.03 Simple disulfide: pdb=" SG CYS d 296 " - pdb=" SG CYS d 331 " distance=2.03 Simple disulfide: pdb=" SG CYS d 378 " - pdb=" SG CYS d 445 " distance=2.03 Simple disulfide: pdb=" SG CYS d 385 " - pdb=" SG CYS d 418 " distance=2.03 Simple disulfide: pdb=" SG CYS d 501 " - pdb=" SG CYS e 605 " distance=2.03 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=2.05 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=2.03 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 C 3 " - " MAN C 4 " " BMA E 3 " - " MAN E 4 " " BMA S 3 " - " MAN S 4 " " BMA m 3 " - " MAN m 4 " " BMA x 3 " - " MAN x 4 " ALPHA1-6 " BMA x 3 " - " MAN x 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " 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 I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " NAG-ASN " NAG A 1 " - " ASN b 392 " " NAG B 1 " - " ASN b 332 " " NAG C 1 " - " ASN b 262 " " NAG D 1 " - " ASN b 156 " " NAG E 1 " - " ASN b 160 " " NAG F 1 " - " ASN b 197 " " NAG G 1 " - " ASN b 234 " " NAG I 1 " - " ASN b 241 " " NAG J 1 " - " ASN b 276 " " NAG K 1 " - " ASN b 301 " " NAG M 1 " - " ASN b 386 " " NAG N 1 " - " ASN b 448 " " NAG O 1 " - " ASN b 465 " " NAG P 1 " - " ASN b 363 " " NAG Q 1 " - " ASN d 392 " " NAG R 1 " - " ASN d 332 " " NAG S 1 " - " ASN d 262 " " NAG T 1 " - " ASN d 156 " " NAG U 1 " - " ASN d 160 " " NAG V 1 " - " ASN d 197 " " NAG W 1 " - " ASN d 234 " " NAG X 1 " - " ASN d 241 " " NAG Y 1 " - " ASN d 276 " " NAG Z 1 " - " ASN d 301 " " NAG a 1 " - " ASN d 386 " " NAG b 601 " - " ASN b 133 " " NAG b 602 " - " ASN b 355 " " NAG b 603 " - " ASN b 269 " " NAG b 604 " - " ASN b 339 " " NAG b 605 " - " ASN b 88 " " NAG b 606 " - " 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 339 " " NAG d 604 " - " ASN d 355 " " NAG d 605 " - " ASN d 269 " " NAG d 606 " - " 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 355 " " NAG f 604 " - " ASN f 269 " " NAG f 605 " - " ASN f 398 " " NAG f 606 " - " ASN f 339 " " NAG g 701 " - " ASN g 611 " " NAG g 702 " - " ASN g 637 " " NAG g 703 " - " ASN g 625 " " NAG h 1 " - " ASN d 448 " " NAG i 1 " - " ASN d 465 " " NAG j 1 " - " ASN d 363 " " NAG k 1 " - " ASN f 392 " " NAG l 1 " - " ASN f 332 " " NAG m 1 " - " ASN f 262 " " NAG n 1 " - " ASN f 156 " " NAG o 1 " - " ASN f 197 " " NAG p 1 " - " ASN f 234 " " NAG q 1 " - " ASN f 241 " " NAG r 1 " - " ASN f 276 " " NAG s 1 " - " ASN f 301 " " NAG t 1 " - " ASN f 363 " " NAG u 1 " - " ASN f 386 " " NAG v 1 " - " ASN f 448 " " NAG w 1 " - " ASN f 465 " " NAG x 1 " - " ASN f 160 " Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 487.4 milliseconds 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 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 31 sheets defined 23.9% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'H' and resid 29 through 33 removed outlier: 3.607A pdb=" N ASN H 32 " --> pdb=" O SER H 29 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN H 33 " --> pdb=" O ILE H 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 29 through 33' Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'H' and resid 112 through 116 removed outlier: 4.362A pdb=" N GLY H 116 " --> pdb=" O TYS H 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.823A pdb=" N VAL L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'b' and resid 70 through 74 Processing helix chain 'b' and resid 98 through 117 removed outlier: 4.225A pdb=" N GLU b 102 " --> pdb=" O ASN b 98 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 126 removed outlier: 3.601A pdb=" N LEU b 125 " --> pdb=" O LEU b 122 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS b 126 " --> pdb=" O THR b 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 122 through 126' Processing helix chain 'b' and resid 334 through 339 Processing helix chain 'b' and resid 341 through 351 removed outlier: 3.583A pdb=" N THR b 351 " --> pdb=" O GLU b 347 " (cutoff:3.500A) Processing helix chain 'b' and resid 368 through 373 Processing helix chain 'b' and resid 387 through 390 Processing helix chain 'b' and resid 475 through 484 removed outlier: 3.860A pdb=" N TRP b 479 " --> pdb=" O MET b 475 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU b 482 " --> pdb=" O ASN b 478 " (cutoff:3.500A) Processing helix chain 'c' and resid 529 through 534 Processing helix chain 'c' and resid 536 through 542 removed outlier: 4.245A pdb=" N GLN c 540 " --> pdb=" O THR c 536 " (cutoff:3.500A) Processing helix chain 'c' and resid 543 through 546 removed outlier: 3.539A pdb=" N SER c 546 " --> pdb=" O GLN c 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 543 through 546' Processing helix chain 'c' and resid 569 through 596 removed outlier: 3.583A pdb=" N LYS c 574 " --> pdb=" O VAL c 570 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU c 592 " --> pdb=" O ARG c 588 " (cutoff:3.500A) Processing helix chain 'c' and resid 619 through 624 Processing helix chain 'c' and resid 627 through 636 removed outlier: 3.840A pdb=" N LYS c 633 " --> pdb=" O LEU c 629 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLU c 634 " --> pdb=" O GLN c 630 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE c 635 " --> pdb=" O TRP c 631 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY c 636 " --> pdb=" O ASP c 632 " (cutoff:3.500A) Processing helix chain 'c' and resid 638 through 658 removed outlier: 3.676A pdb=" N GLU c 647 " --> pdb=" O TYR c 643 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU c 648 " --> pdb=" O ARG c 644 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER c 649 " --> pdb=" O LEU c 645 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 74 Processing helix chain 'd' and resid 98 through 116 removed outlier: 4.008A pdb=" N GLU d 102 " --> pdb=" O ASN d 98 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR d 106 " --> pdb=" O GLU d 102 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU d 116 " --> pdb=" O TRP d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 122 through 126 removed outlier: 3.599A pdb=" N LEU d 125 " --> pdb=" O LEU d 122 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS d 126 " --> pdb=" O THR d 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 122 through 126' Processing helix chain 'd' and resid 334 through 351 removed outlier: 3.516A pdb=" N LYS d 340 " --> pdb=" O SER d 336 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN d 343 " --> pdb=" O ASN d 339 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR d 351 " --> pdb=" O GLU d 347 " (cutoff:3.500A) Processing helix chain 'd' and resid 368 through 373 Processing helix chain 'd' and resid 387 through 390 Processing helix chain 'd' and resid 475 through 484 removed outlier: 4.208A pdb=" N TRP d 479 " --> pdb=" O MET d 475 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU d 482 " --> pdb=" O ASN d 478 " (cutoff:3.500A) Processing helix chain 'e' and resid 523 through 527 removed outlier: 4.571A pdb=" N GLY e 527 " --> pdb=" O GLY e 524 " (cutoff:3.500A) Processing helix chain 'e' and resid 529 through 534 Processing helix chain 'e' and resid 536 through 542 removed outlier: 4.240A pdb=" N GLN e 540 " --> pdb=" O THR e 536 " (cutoff:3.500A) Processing helix chain 'e' and resid 569 through 597 removed outlier: 3.634A pdb=" N LYS e 574 " --> pdb=" O VAL e 570 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU e 592 " --> pdb=" O ARG e 588 " (cutoff:3.500A) Processing helix chain 'e' and resid 619 through 624 removed outlier: 3.594A pdb=" N TRP e 623 " --> pdb=" O LEU e 619 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN e 624 " --> pdb=" O ASP e 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 619 through 624' Processing helix chain 'e' and resid 627 through 633 removed outlier: 3.548A pdb=" N LYS e 633 " --> pdb=" O LEU e 629 " (cutoff:3.500A) Processing helix chain 'e' and resid 635 through 658 removed outlier: 4.316A pdb=" N GLN e 640 " --> pdb=" O GLY e 636 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU e 641 " --> pdb=" O ASN e 637 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG e 644 " --> pdb=" O GLN e 640 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 74 Processing helix chain 'f' and resid 98 through 117 removed outlier: 4.272A pdb=" N GLU f 102 " --> pdb=" O ASN f 98 " (cutoff:3.500A) Processing helix chain 'f' and resid 122 through 126 removed outlier: 3.589A pdb=" N LEU f 125 " --> pdb=" O LEU f 122 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS f 126 " --> pdb=" O THR f 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 122 through 126' Processing helix chain 'f' and resid 334 through 351 removed outlier: 3.561A pdb=" N LYS f 340 " --> pdb=" O SER f 336 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN f 343 " --> pdb=" O ASN f 339 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR f 351 " --> pdb=" O GLU f 347 " (cutoff:3.500A) Processing helix chain 'f' and resid 368 through 373 removed outlier: 3.598A pdb=" N THR f 373 " --> pdb=" O LEU f 369 " (cutoff:3.500A) Processing helix chain 'f' and resid 387 through 390 Processing helix chain 'f' and resid 475 through 481 removed outlier: 4.140A 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 542 removed outlier: 4.177A pdb=" N GLN g 540 " --> pdb=" O THR g 536 " (cutoff:3.500A) Processing helix chain 'g' and resid 569 through 596 removed outlier: 3.597A pdb=" N LYS g 574 " --> pdb=" O VAL g 570 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU g 592 " --> pdb=" O ARG g 588 " (cutoff:3.500A) Processing helix chain 'g' and resid 618 through 625 removed outlier: 3.568A pdb=" N TRP g 623 " --> pdb=" O LEU g 619 " (cutoff:3.500A) Processing helix chain 'g' and resid 627 through 636 removed outlier: 3.614A pdb=" N LYS g 633 " --> pdb=" O LEU g 629 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU g 634 " --> pdb=" O GLN g 630 " (cutoff:3.500A) Processing helix chain 'g' and resid 638 through 658 removed outlier: 3.935A pdb=" N ARG g 644 " --> pdb=" O GLN g 640 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 12 through 13 removed outlier: 4.154A pdb=" N TYR H 34 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY H 50 " --> pdb=" O TRP H 37 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG H 39 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N TRP H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 12 through 13 removed outlier: 7.021A pdb=" N CYS H 98 " --> pdb=" O TRP H 128 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TRP H 128 " --> pdb=" O CYS H 98 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ARG H 100 " --> pdb=" O ASP H 126 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP H 126 " --> pdb=" O ARG H 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 105 through 106 removed outlier: 6.853A pdb=" N TYR H 118 " --> pdb=" O ARG f 169 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N LYS f 171 " --> pdb=" O TYR H 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.869A pdb=" N ASP L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.663A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TYR L 49 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.663A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR L 98 " --> pdb=" O HIS L 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 494 through 499 removed outlier: 5.453A pdb=" N VAL c 608 " --> pdb=" O VAL b 36 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL b 38 " --> pdb=" O THR c 606 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR c 606 " --> pdb=" O VAL b 38 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N TYR b 40 " --> pdb=" O CYS c 604 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N CYS c 604 " --> pdb=" O TYR b 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 45 through 47 removed outlier: 4.818A pdb=" N VAL b 242 " --> pdb=" O LEU b 86 " (cutoff:3.500A) 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 169 through 177 Processing sheet with id=AB3, first strand: chain 'b' and resid 202 through 203 removed outlier: 6.255A pdb=" N THR b 202 " --> pdb=" O TYR b 435 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'b' and resid 259 through 261 removed outlier: 10.105A pdb=" N LYS b 444 " --> pdb=" O ILE b 294 " (cutoff:3.500A) removed outlier: 11.417A pdb=" N ILE b 294 " --> pdb=" O LYS b 444 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N GLU b 446 " --> pdb=" O VAL b 292 " (cutoff:3.500A) removed outlier: 10.585A pdb=" N VAL b 292 " --> pdb=" O GLU b 446 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N ASN b 448 " --> pdb=" O GLN b 290 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N GLN b 290 " --> pdb=" O ASN b 448 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR b 450 " --> pdb=" O LEU b 288 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS b 330 " --> pdb=" O ILE b 297 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS b 421 " --> pdb=" O PHE b 382 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N PHE b 382 " --> pdb=" O LYS b 421 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'b' and resid 271 through 273 removed outlier: 6.560A pdb=" N THR b 450 " --> pdb=" O LEU b 288 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N GLN b 290 " --> pdb=" O ASN b 448 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N ASN b 448 " --> pdb=" O GLN b 290 " (cutoff:3.500A) removed outlier: 10.585A pdb=" N VAL b 292 " --> pdb=" O GLU b 446 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N GLU b 446 " --> pdb=" O VAL b 292 " (cutoff:3.500A) removed outlier: 11.417A pdb=" N ILE b 294 " --> pdb=" O LYS b 444 " (cutoff:3.500A) removed outlier: 10.105A pdb=" N LYS b 444 " --> pdb=" O ILE b 294 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR b 357 " --> pdb=" O GLU b 466 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N PHE b 468 " --> pdb=" O THR b 357 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE b 359 " --> pdb=" O PHE b 468 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'b' and resid 302 through 312 removed outlier: 6.492A pdb=" N THR b 303 " --> pdb=" O GLY b 321 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLN b 315 " --> pdb=" O ILE b 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'd' and resid 494 through 499 removed outlier: 5.467A pdb=" N VAL e 608 " --> pdb=" O VAL d 36 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N VAL d 38 " --> pdb=" O THR e 606 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N THR e 606 " --> pdb=" O VAL d 38 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N TYR d 40 " --> pdb=" O CYS e 604 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N CYS e 604 " --> pdb=" O TYR d 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'd' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'd' and resid 91 through 94 Processing sheet with id=AC1, first strand: chain 'd' and resid 169 through 177 Processing sheet with id=AC2, first strand: chain 'd' and resid 202 through 203 removed outlier: 6.360A pdb=" N THR d 202 " --> pdb=" O TYR d 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'd' and resid 259 through 261 removed outlier: 10.006A pdb=" N LYS d 444 " --> pdb=" O ILE d 294 " (cutoff:3.500A) removed outlier: 11.394A pdb=" N ILE d 294 " --> pdb=" O LYS d 444 " (cutoff:3.500A) removed outlier: 9.699A pdb=" N GLU d 446 " --> pdb=" O VAL d 292 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N VAL d 292 " --> pdb=" O GLU d 446 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N ASN d 448 " --> pdb=" O GLN d 290 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N GLN d 290 " --> pdb=" O ASN d 448 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR d 450 " --> pdb=" O LEU d 288 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS d 330 " --> pdb=" O ILE d 297 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS d 421 " --> pdb=" O PHE d 382 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE d 382 " --> pdb=" O LYS d 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'd' and resid 271 through 273 removed outlier: 6.529A pdb=" N THR d 450 " --> pdb=" O LEU d 288 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N GLN d 290 " --> pdb=" O ASN d 448 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N ASN d 448 " --> pdb=" O GLN d 290 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N VAL d 292 " --> pdb=" O GLU d 446 " (cutoff:3.500A) removed outlier: 9.699A pdb=" N GLU d 446 " --> pdb=" O VAL d 292 " (cutoff:3.500A) removed outlier: 11.394A pdb=" N ILE d 294 " --> pdb=" O LYS d 444 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N LYS d 444 " --> pdb=" O ILE d 294 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR d 357 " --> pdb=" O GLU d 466 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE d 468 " --> pdb=" O THR d 357 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE d 359 " --> pdb=" O PHE d 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'd' and resid 302 through 312 removed outlier: 6.397A pdb=" N THR d 303 " --> pdb=" O GLY d 321 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLN d 315 " --> pdb=" O ILE d 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'f' and resid 494 through 499 removed outlier: 5.357A pdb=" N VAL g 608 " --> pdb=" O VAL f 36 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL f 38 " --> pdb=" O THR g 606 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N THR g 606 " --> pdb=" O VAL f 38 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N TYR f 40 " --> pdb=" O CYS g 604 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N CYS g 604 " --> pdb=" O TYR f 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'f' and resid 45 through 47 Processing sheet with id=AC8, first strand: chain 'f' and resid 75 through 76 removed outlier: 3.782A pdb=" N VAL f 75 " --> pdb=" O CYS f 54 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'f' and resid 91 through 94 Processing sheet with id=AD1, first strand: chain 'f' and resid 202 through 203 removed outlier: 6.254A pdb=" N THR f 202 " --> pdb=" O TYR f 435 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'f' and resid 259 through 261 removed outlier: 6.449A pdb=" N LEU f 260 " --> pdb=" O THR f 450 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N LYS f 444 " --> pdb=" O ILE f 294 " (cutoff:3.500A) removed outlier: 11.431A pdb=" N ILE f 294 " --> pdb=" O LYS f 444 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N GLU f 446 " --> pdb=" O VAL f 292 " (cutoff:3.500A) removed outlier: 10.660A pdb=" N VAL f 292 " --> pdb=" O GLU f 446 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N ASN f 448 " --> pdb=" O GLN f 290 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N GLN f 290 " --> pdb=" O ASN f 448 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR f 450 " --> pdb=" O LEU f 288 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS f 330 " --> pdb=" O ILE f 297 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA f 329 " --> pdb=" O CYS f 418 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS f 421 " --> pdb=" O PHE f 382 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE f 382 " --> pdb=" O LYS f 421 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'f' and resid 271 through 273 removed outlier: 6.588A pdb=" N THR f 450 " --> pdb=" O LEU f 288 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N GLN f 290 " --> pdb=" O ASN f 448 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N ASN f 448 " --> pdb=" O GLN f 290 " (cutoff:3.500A) removed outlier: 10.660A pdb=" N VAL f 292 " --> pdb=" O GLU f 446 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N GLU f 446 " --> pdb=" O VAL f 292 " (cutoff:3.500A) removed outlier: 11.431A pdb=" N ILE f 294 " --> pdb=" O LYS f 444 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N LYS f 444 " --> pdb=" O ILE f 294 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'f' and resid 301 through 312 removed outlier: 6.847A pdb=" N ASN f 301 " --> pdb=" O ILE f 323 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE f 323 " --> pdb=" O ASN f 301 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N THR f 303 " --> pdb=" O GLY f 321 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLN f 315 " --> pdb=" O ILE f 309 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1524 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: 2.77 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3039 1.33 - 1.46: 5377 1.46 - 1.58: 9068 1.58 - 1.71: 2 1.71 - 1.84: 136 Bond restraints: 17622 Sorted by residual: bond pdb=" CA SER d 364 " pdb=" CB SER d 364 " ideal model delta sigma weight residual 1.528 1.457 0.071 1.50e-02 4.44e+03 2.24e+01 bond pdb=" CA ALA d 219 " pdb=" CB ALA d 219 " ideal model delta sigma weight residual 1.534 1.480 0.054 1.30e-02 5.92e+03 1.72e+01 bond pdb=" CA SER b 264 " pdb=" CB SER b 264 " ideal model delta sigma weight residual 1.530 1.471 0.059 1.58e-02 4.01e+03 1.41e+01 bond pdb=" C ASN c 637 " pdb=" N TYR c 638 " ideal model delta sigma weight residual 1.333 1.386 -0.053 1.45e-02 4.76e+03 1.35e+01 bond pdb=" CA TYR c 638 " pdb=" CB TYR c 638 " ideal model delta sigma weight residual 1.531 1.584 -0.054 1.59e-02 3.96e+03 1.13e+01 ... (remaining 17617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 23294 2.84 - 5.68: 578 5.68 - 8.53: 35 8.53 - 11.37: 2 11.37 - 14.21: 2 Bond angle restraints: 23911 Sorted by residual: angle pdb=" N TYR c 638 " pdb=" CA TYR c 638 " pdb=" CB TYR c 638 " ideal model delta sigma weight residual 110.26 96.05 14.21 1.49e+00 4.50e-01 9.10e+01 angle pdb=" O ASN c 637 " pdb=" C ASN c 637 " pdb=" N TYR c 638 " ideal model delta sigma weight residual 122.27 133.42 -11.15 1.23e+00 6.61e-01 8.21e+01 angle pdb=" CA ASN c 637 " pdb=" C ASN c 637 " pdb=" N TYR c 638 " ideal model delta sigma weight residual 117.72 106.44 11.28 1.31e+00 5.83e-01 7.41e+01 angle pdb=" N TYR d 217 " pdb=" CA TYR d 217 " pdb=" CB TYR d 217 " ideal model delta sigma weight residual 110.42 122.18 -11.76 1.63e+00 3.76e-01 5.20e+01 angle pdb=" CA HIS d 216 " pdb=" C HIS d 216 " pdb=" O HIS d 216 " ideal model delta sigma weight residual 120.38 113.36 7.02 1.09e+00 8.42e-01 4.15e+01 ... (remaining 23906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.05: 11428 21.05 - 42.11: 562 42.11 - 63.16: 159 63.16 - 84.22: 64 84.22 - 105.27: 31 Dihedral angle restraints: 12244 sinusoidal: 6589 harmonic: 5655 Sorted by residual: dihedral pdb=" CB CYS f 54 " pdb=" SG CYS f 54 " pdb=" SG CYS f 74 " pdb=" CB CYS f 74 " ideal model delta sinusoidal sigma weight residual 93.00 4.88 88.12 1 1.00e+01 1.00e-02 9.29e+01 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 93.00 157.86 -64.86 1 1.00e+01 1.00e-02 5.52e+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 93.00 154.91 -61.91 1 1.00e+01 1.00e-02 5.08e+01 ... (remaining 12241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2792 0.104 - 0.209: 206 0.209 - 0.313: 25 0.313 - 0.417: 9 0.417 - 0.522: 2 Chirality restraints: 3034 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-02 2.50e+03 4.22e+02 chirality pdb=" C1 NAG m 2 " pdb=" O4 NAG m 1 " pdb=" C2 NAG m 2 " pdb=" O5 NAG m 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-02 2.50e+03 3.30e+02 chirality pdb=" C1 NAG t 2 " pdb=" O4 NAG t 1 " pdb=" C2 NAG t 2 " pdb=" O5 NAG t 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.83e+02 ... (remaining 3031 not shown) Planarity restraints: 2938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 605 " 0.288 2.00e-02 2.50e+03 2.47e-01 7.62e+02 pdb=" C7 NAG f 605 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG f 605 " 0.164 2.00e-02 2.50e+03 pdb=" N2 NAG f 605 " -0.433 2.00e-02 2.50e+03 pdb=" O7 NAG f 605 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 606 " 0.250 2.00e-02 2.50e+03 2.14e-01 5.71e+02 pdb=" C7 NAG d 606 " -0.059 2.00e-02 2.50e+03 pdb=" C8 NAG d 606 " 0.157 2.00e-02 2.50e+03 pdb=" N2 NAG d 606 " -0.370 2.00e-02 2.50e+03 pdb=" O7 NAG d 606 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 605 " -0.217 2.00e-02 2.50e+03 1.86e-01 4.30e+02 pdb=" C7 NAG b 605 " 0.049 2.00e-02 2.50e+03 pdb=" C8 NAG b 605 " 0.031 2.00e-02 2.50e+03 pdb=" N2 NAG b 605 " 0.305 2.00e-02 2.50e+03 pdb=" O7 NAG b 605 " -0.168 2.00e-02 2.50e+03 ... (remaining 2935 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2794 2.77 - 3.30: 16385 3.30 - 3.84: 27105 3.84 - 4.37: 32491 4.37 - 4.90: 56539 Nonbonded interactions: 135314 Sorted by model distance: nonbonded pdb=" OE2 GLU e 654 " pdb=" NZ LYS e 658 " model vdw 2.238 3.120 nonbonded pdb=" O SER e 612 " pdb=" ND2 ASN e 616 " model vdw 2.266 3.120 nonbonded pdb=" OG SER L 14 " pdb=" OD2 ASP L 17 " model vdw 2.266 3.040 nonbonded pdb=" O THR g 536 " pdb=" OG1 THR g 536 " model vdw 2.297 3.040 nonbonded pdb=" NZ LYS d 460 " pdb=" OD1 ASN d 462 " model vdw 2.332 3.120 ... (remaining 135309 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'R' selection = chain 'X' selection = chain 'l' selection = chain 'q' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'S' selection = chain 'm' } ncs_group { reference = chain 'b' selection = chain 'd' selection = chain 'f' } 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: 4.600 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.900 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:9.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 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 : 0.006 0.071 17788 Z= 0.302 Angle : 1.111 18.300 24371 Z= 0.571 Chirality : 0.060 0.522 3034 Planarity : 0.010 0.247 2869 Dihedral : 14.675 105.272 8480 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.47 % 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: -1.21 (0.19), residues: 1915 helix: -0.40 (0.28), residues: 384 sheet: -0.74 (0.22), residues: 509 loop : -0.91 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG e 588 TYR 0.020 0.001 TYR g 638 PHE 0.018 0.001 PHE b 210 TRP 0.026 0.002 TRP b 338 HIS 0.013 0.001 HIS d 216 Details of bonding type rmsd covalent geometry : bond 0.00519 (17622) covalent geometry : angle 0.95681 (23911) SS BOND : bond 0.00375 ( 38) SS BOND : angle 1.18088 ( 76) hydrogen bonds : bond 0.23281 ( 550) hydrogen bonds : angle 8.04002 ( 1524) link_ALPHA1-3 : bond 0.04543 ( 5) link_ALPHA1-3 : angle 6.94985 ( 15) link_ALPHA1-6 : bond 0.03672 ( 1) link_ALPHA1-6 : angle 4.93234 ( 3) link_BETA1-4 : bond 0.03210 ( 53) link_BETA1-4 : angle 5.67354 ( 159) link_NAG-ASN : bond 0.00666 ( 69) link_NAG-ASN : angle 3.25434 ( 207) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: L 17 ASP cc_start: 0.8253 (m-30) cc_final: 0.7993 (m-30) REVERT: L 106 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8138 (mm-30) REVERT: b 467 THR cc_start: 0.8797 (p) cc_final: 0.8569 (p) REVERT: c 584 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8394 (mt-10) REVERT: c 588 ARG cc_start: 0.7997 (tpp80) cc_final: 0.7760 (tmm-80) REVERT: c 599 SER cc_start: 0.8995 (t) cc_final: 0.8735 (m) REVERT: c 621 GLU cc_start: 0.8681 (pt0) cc_final: 0.8472 (pp20) REVERT: d 492 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8199 (mm-30) REVERT: e 567 LYS cc_start: 0.8132 (mttt) cc_final: 0.7599 (mmtt) REVERT: e 585 ARG cc_start: 0.8771 (mmm160) cc_final: 0.8523 (mtp-110) REVERT: e 621 GLU cc_start: 0.8818 (pt0) cc_final: 0.8439 (pp20) REVERT: f 267 GLU cc_start: 0.8360 (pm20) cc_final: 0.8004 (pm20) REVERT: f 322 ASP cc_start: 0.8439 (p0) cc_final: 0.8220 (p0) REVERT: g 584 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8724 (mt-10) REVERT: g 617 LYS cc_start: 0.9179 (mttm) cc_final: 0.8886 (mtpm) REVERT: g 626 MET cc_start: 0.8201 (ttp) cc_final: 0.7841 (ttm) REVERT: g 657 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8064 (mt-10) outliers start: 0 outliers final: 1 residues processed: 182 average time/residue: 0.6405 time to fit residues: 128.7018 Evaluate side-chains 136 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 535 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 330 HIS ** b 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 330 HIS f 130 HIS f 330 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.081882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.057892 restraints weight = 39985.959| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 4.13 r_work: 0.2718 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 17788 Z= 0.257 Angle : 0.832 11.549 24371 Z= 0.374 Chirality : 0.049 0.332 3034 Planarity : 0.004 0.046 2869 Dihedral : 9.870 73.179 4766 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.82 % Favored : 97.13 % Rotamer: Outliers : 1.85 % Allowed : 11.98 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: -0.95 (0.19), residues: 1915 helix: -0.17 (0.27), residues: 390 sheet: -0.66 (0.22), residues: 527 loop : -0.69 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG e 588 TYR 0.014 0.002 TYR H 97 PHE 0.018 0.002 PHE f 383 TRP 0.015 0.002 TRP b 338 HIS 0.004 0.001 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00617 (17622) covalent geometry : angle 0.75054 (23911) SS BOND : bond 0.00359 ( 38) SS BOND : angle 1.09413 ( 76) hydrogen bonds : bond 0.05902 ( 550) hydrogen bonds : angle 5.68224 ( 1524) link_ALPHA1-3 : bond 0.01015 ( 5) link_ALPHA1-3 : angle 2.48183 ( 15) link_ALPHA1-6 : bond 0.00223 ( 1) link_ALPHA1-6 : angle 1.25406 ( 3) link_BETA1-4 : bond 0.00617 ( 53) link_BETA1-4 : angle 3.55342 ( 159) link_NAG-ASN : bond 0.00435 ( 69) link_NAG-ASN : angle 2.39944 ( 207) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: H 84 ARG cc_start: 0.8374 (mtm110) cc_final: 0.7757 (ptp-110) REVERT: L 17 ASP cc_start: 0.8194 (m-30) cc_final: 0.7894 (m-30) REVERT: L 106 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8061 (mm-30) REVERT: c 588 ARG cc_start: 0.8057 (tpp80) cc_final: 0.7783 (tmm-80) REVERT: c 599 SER cc_start: 0.9076 (t) cc_final: 0.8773 (m) REVERT: c 621 GLU cc_start: 0.8842 (pt0) cc_final: 0.8522 (pp20) REVERT: c 638 TYR cc_start: 0.8271 (m-80) cc_final: 0.8051 (m-80) REVERT: c 644 ARG cc_start: 0.8194 (mmp80) cc_final: 0.7904 (tpp80) REVERT: d 95 MET cc_start: 0.9275 (ptt) cc_final: 0.8960 (ptm) REVERT: d 492 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8289 (mm-30) REVERT: e 567 LYS cc_start: 0.8143 (mttt) cc_final: 0.7538 (mmtt) REVERT: e 621 GLU cc_start: 0.8799 (pt0) cc_final: 0.8407 (pp20) REVERT: f 322 ASP cc_start: 0.8621 (p0) cc_final: 0.8326 (p0) REVERT: f 424 ILE cc_start: 0.9103 (pt) cc_final: 0.8751 (pp) REVERT: g 567 LYS cc_start: 0.8242 (mmtm) cc_final: 0.7428 (tppp) REVERT: g 617 LYS cc_start: 0.9077 (mttm) cc_final: 0.8681 (mtpm) outliers start: 32 outliers final: 11 residues processed: 156 average time/residue: 0.6955 time to fit residues: 119.7045 Evaluate side-chains 138 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain c residue 568 LEU Chi-restraints excluded: chain c residue 612 SER Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain f residue 286 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 15 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 58 optimal weight: 0.0870 chunk 139 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 185 ASN e 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.083836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.060013 restraints weight = 40030.833| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 4.15 r_work: 0.2772 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17788 Z= 0.119 Angle : 0.696 11.078 24371 Z= 0.309 Chirality : 0.046 0.293 3034 Planarity : 0.003 0.045 2869 Dihedral : 8.550 64.374 4764 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.56 % Favored : 97.39 % Rotamer: Outliers : 1.97 % Allowed : 13.19 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: -0.60 (0.19), residues: 1915 helix: 0.09 (0.28), residues: 390 sheet: -0.41 (0.21), residues: 536 loop : -0.48 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG e 588 TYR 0.010 0.001 TYR L 49 PHE 0.009 0.001 PHE b 383 TRP 0.012 0.001 TRP f 338 HIS 0.002 0.000 HIS d 216 Details of bonding type rmsd covalent geometry : bond 0.00262 (17622) covalent geometry : angle 0.61972 (23911) SS BOND : bond 0.00193 ( 38) SS BOND : angle 0.69132 ( 76) hydrogen bonds : bond 0.04664 ( 550) hydrogen bonds : angle 5.18211 ( 1524) link_ALPHA1-3 : bond 0.01202 ( 5) link_ALPHA1-3 : angle 2.47547 ( 15) link_ALPHA1-6 : bond 0.00354 ( 1) link_ALPHA1-6 : angle 1.44602 ( 3) link_BETA1-4 : bond 0.00630 ( 53) link_BETA1-4 : angle 3.24214 ( 159) link_NAG-ASN : bond 0.00318 ( 69) link_NAG-ASN : angle 2.00302 ( 207) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 71 SER cc_start: 0.8800 (t) cc_final: 0.8462 (p) REVERT: L 17 ASP cc_start: 0.8176 (m-30) cc_final: 0.7867 (m-30) REVERT: L 106 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8071 (mm-30) REVERT: c 530 MET cc_start: 0.8025 (mtt) cc_final: 0.7716 (mtt) REVERT: c 588 ARG cc_start: 0.7995 (tpp80) cc_final: 0.7772 (tmm-80) REVERT: c 599 SER cc_start: 0.9060 (t) cc_final: 0.8762 (m) REVERT: c 621 GLU cc_start: 0.8801 (pt0) cc_final: 0.8566 (pp20) REVERT: c 638 TYR cc_start: 0.8303 (m-80) cc_final: 0.7972 (m-80) REVERT: c 644 ARG cc_start: 0.8154 (mmp80) cc_final: 0.7773 (tpp80) REVERT: d 445 CYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7919 (p) REVERT: d 475 MET cc_start: 0.8656 (tpp) cc_final: 0.8387 (tpp) REVERT: e 567 LYS cc_start: 0.8169 (mttt) cc_final: 0.7559 (mmtt) REVERT: e 588 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7700 (tmm-80) REVERT: f 322 ASP cc_start: 0.8604 (p0) cc_final: 0.8301 (p0) REVERT: g 567 LYS cc_start: 0.8202 (mmtm) cc_final: 0.7400 (tppp) REVERT: g 617 LYS cc_start: 0.9078 (mttm) cc_final: 0.8658 (mtpm) REVERT: g 657 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7685 (mt-10) outliers start: 34 outliers final: 14 residues processed: 156 average time/residue: 0.6583 time to fit residues: 113.9703 Evaluate side-chains 139 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain c residue 568 LEU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain e residue 648 GLU Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain g residue 604 CYS Chi-restraints excluded: chain g residue 638 TYR Chi-restraints excluded: chain g residue 657 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 64 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 195 ASN b 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.083066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.059288 restraints weight = 40007.376| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 4.13 r_work: 0.2750 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17788 Z= 0.138 Angle : 0.677 10.566 24371 Z= 0.301 Chirality : 0.045 0.288 3034 Planarity : 0.003 0.039 2869 Dihedral : 7.961 60.767 4764 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.28 % Rotamer: Outliers : 2.26 % Allowed : 13.66 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: -0.46 (0.19), residues: 1915 helix: 0.17 (0.28), residues: 390 sheet: -0.25 (0.21), residues: 542 loop : -0.42 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG e 588 TYR 0.010 0.001 TYR L 49 PHE 0.010 0.001 PHE f 383 TRP 0.011 0.001 TRP f 338 HIS 0.003 0.001 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00320 (17622) covalent geometry : angle 0.60696 (23911) SS BOND : bond 0.00252 ( 38) SS BOND : angle 0.71208 ( 76) hydrogen bonds : bond 0.04210 ( 550) hydrogen bonds : angle 4.99465 ( 1524) link_ALPHA1-3 : bond 0.01232 ( 5) link_ALPHA1-3 : angle 2.48969 ( 15) link_ALPHA1-6 : bond 0.00424 ( 1) link_ALPHA1-6 : angle 1.37040 ( 3) link_BETA1-4 : bond 0.00606 ( 53) link_BETA1-4 : angle 3.07775 ( 159) link_NAG-ASN : bond 0.00267 ( 69) link_NAG-ASN : angle 1.88291 ( 207) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 14 LYS cc_start: 0.8586 (mtpm) cc_final: 0.8232 (mmtt) REVERT: H 71 SER cc_start: 0.8733 (t) cc_final: 0.8397 (p) REVERT: L 17 ASP cc_start: 0.8207 (m-30) cc_final: 0.7861 (m-30) REVERT: L 106 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8045 (mm-30) REVERT: b 187 ASN cc_start: 0.8232 (t0) cc_final: 0.8028 (t0) REVERT: c 530 MET cc_start: 0.8053 (mtt) cc_final: 0.7715 (mtt) REVERT: c 599 SER cc_start: 0.9074 (t) cc_final: 0.8772 (m) REVERT: c 621 GLU cc_start: 0.8806 (pt0) cc_final: 0.8565 (pp20) REVERT: c 638 TYR cc_start: 0.8365 (m-80) cc_final: 0.8145 (m-80) REVERT: c 644 ARG cc_start: 0.8147 (mmp80) cc_final: 0.7766 (tpp80) REVERT: d 475 MET cc_start: 0.8705 (tpp) cc_final: 0.8384 (tpp) REVERT: e 567 LYS cc_start: 0.8194 (mttt) cc_final: 0.7565 (mmtt) REVERT: e 588 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7719 (tmm-80) REVERT: e 620 ASP cc_start: 0.8910 (t0) cc_final: 0.8259 (p0) REVERT: f 322 ASP cc_start: 0.8638 (p0) cc_final: 0.8349 (p0) REVERT: g 567 LYS cc_start: 0.8183 (mmtm) cc_final: 0.7391 (tppp) REVERT: g 617 LYS cc_start: 0.9095 (mttm) cc_final: 0.8622 (mtpm) REVERT: g 657 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7444 (mt-10) outliers start: 39 outliers final: 20 residues processed: 161 average time/residue: 0.6246 time to fit residues: 111.7236 Evaluate side-chains 144 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain c residue 568 LEU 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 d residue 445 CYS Chi-restraints excluded: chain e residue 648 GLU Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 428 GLN Chi-restraints excluded: chain g residue 544 LEU Chi-restraints excluded: chain g residue 638 TYR Chi-restraints excluded: chain g residue 657 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 143 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 616 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.082406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.058746 restraints weight = 39826.914| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 4.11 r_work: 0.2746 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17788 Z= 0.158 Angle : 0.677 10.119 24371 Z= 0.302 Chirality : 0.045 0.293 3034 Planarity : 0.003 0.037 2869 Dihedral : 7.792 59.792 4764 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.87 % Favored : 97.08 % Rotamer: Outliers : 2.49 % Allowed : 14.47 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: -0.30 (0.19), residues: 1915 helix: 0.45 (0.29), residues: 372 sheet: -0.22 (0.21), residues: 542 loop : -0.33 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG c 588 TYR 0.014 0.001 TYR H 110 PHE 0.010 0.001 PHE f 383 TRP 0.011 0.001 TRP f 338 HIS 0.003 0.001 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00374 (17622) covalent geometry : angle 0.61032 (23911) SS BOND : bond 0.00385 ( 38) SS BOND : angle 0.76152 ( 76) hydrogen bonds : bond 0.04165 ( 550) hydrogen bonds : angle 4.90917 ( 1524) link_ALPHA1-3 : bond 0.01166 ( 5) link_ALPHA1-3 : angle 2.56107 ( 15) link_ALPHA1-6 : bond 0.00407 ( 1) link_ALPHA1-6 : angle 1.35670 ( 3) link_BETA1-4 : bond 0.00585 ( 53) link_BETA1-4 : angle 2.98082 ( 159) link_NAG-ASN : bond 0.00268 ( 69) link_NAG-ASN : angle 1.84373 ( 207) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 14 LYS cc_start: 0.8625 (mtpm) cc_final: 0.8279 (mmtt) REVERT: H 71 SER cc_start: 0.8718 (t) cc_final: 0.8348 (p) REVERT: L 17 ASP cc_start: 0.8150 (m-30) cc_final: 0.7796 (m-30) REVERT: L 106 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8089 (mm-30) REVERT: b 187 ASN cc_start: 0.8315 (t0) cc_final: 0.8087 (t0) REVERT: c 530 MET cc_start: 0.7972 (mtt) cc_final: 0.7652 (mtt) REVERT: c 599 SER cc_start: 0.9081 (t) cc_final: 0.8768 (m) REVERT: c 621 GLU cc_start: 0.8790 (pt0) cc_final: 0.8508 (pp20) REVERT: c 644 ARG cc_start: 0.8155 (mmp80) cc_final: 0.7877 (tpp80) REVERT: d 475 MET cc_start: 0.8716 (tpp) cc_final: 0.8405 (tpp) REVERT: d 491 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8721 (tt) REVERT: e 567 LYS cc_start: 0.8177 (mttt) cc_final: 0.7544 (mmtt) REVERT: e 588 ARG cc_start: 0.7954 (ttm-80) cc_final: 0.7681 (tmm-80) REVERT: e 617 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8932 (mtpm) REVERT: f 322 ASP cc_start: 0.8605 (p0) cc_final: 0.8334 (p0) REVERT: g 567 LYS cc_start: 0.8143 (mmtm) cc_final: 0.7360 (tppp) REVERT: g 617 LYS cc_start: 0.9078 (mttm) cc_final: 0.8549 (mtpm) REVERT: g 657 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7451 (mt-10) outliers start: 43 outliers final: 22 residues processed: 162 average time/residue: 0.6286 time to fit residues: 113.1690 Evaluate side-chains 152 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain c residue 568 LEU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 378 CYS Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain e residue 617 LYS Chi-restraints excluded: chain e residue 648 GLU Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 428 GLN Chi-restraints excluded: chain g residue 544 LEU Chi-restraints excluded: chain g residue 626 MET Chi-restraints excluded: chain g residue 638 TYR Chi-restraints excluded: chain g residue 657 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 163 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 188 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.081281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.057706 restraints weight = 40061.721| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 4.09 r_work: 0.2715 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17788 Z= 0.201 Angle : 0.705 10.156 24371 Z= 0.316 Chirality : 0.046 0.312 3034 Planarity : 0.003 0.037 2869 Dihedral : 7.841 61.542 4764 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 3.12 % Allowed : 14.35 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: 1915 helix: 0.45 (0.29), residues: 372 sheet: -0.22 (0.21), residues: 543 loop : -0.35 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG e 644 TYR 0.012 0.001 TYR L 49 PHE 0.013 0.002 PHE f 383 TRP 0.011 0.001 TRP f 338 HIS 0.009 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00482 (17622) covalent geometry : angle 0.64246 (23911) SS BOND : bond 0.00279 ( 38) SS BOND : angle 0.80742 ( 76) hydrogen bonds : bond 0.04321 ( 550) hydrogen bonds : angle 4.92836 ( 1524) link_ALPHA1-3 : bond 0.00993 ( 5) link_ALPHA1-3 : angle 2.44994 ( 15) link_ALPHA1-6 : bond 0.00348 ( 1) link_ALPHA1-6 : angle 1.33229 ( 3) link_BETA1-4 : bond 0.00565 ( 53) link_BETA1-4 : angle 2.93628 ( 159) link_NAG-ASN : bond 0.00315 ( 69) link_NAG-ASN : angle 1.86602 ( 207) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 131 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 71 SER cc_start: 0.8738 (t) cc_final: 0.8406 (p) REVERT: L 17 ASP cc_start: 0.8193 (m-30) cc_final: 0.7789 (m-30) REVERT: L 106 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8052 (mm-30) REVERT: b 187 ASN cc_start: 0.8405 (t0) cc_final: 0.7906 (t0) REVERT: c 530 MET cc_start: 0.8021 (mtt) cc_final: 0.7712 (mtt) REVERT: c 599 SER cc_start: 0.9068 (t) cc_final: 0.8743 (m) REVERT: c 621 GLU cc_start: 0.8853 (pt0) cc_final: 0.8542 (pp20) REVERT: d 475 MET cc_start: 0.8764 (tpp) cc_final: 0.8471 (tpp) REVERT: d 491 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8573 (tt) REVERT: d 492 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8370 (mm-30) REVERT: e 567 LYS cc_start: 0.8123 (mttt) cc_final: 0.7497 (mmtt) REVERT: e 588 ARG cc_start: 0.8024 (ttm-80) cc_final: 0.7749 (tmm-80) REVERT: f 322 ASP cc_start: 0.8616 (p0) cc_final: 0.8334 (p0) REVERT: g 567 LYS cc_start: 0.8150 (mmtm) cc_final: 0.7339 (tppp) REVERT: g 617 LYS cc_start: 0.9061 (mttm) cc_final: 0.8504 (mtpm) REVERT: g 657 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7466 (mt-10) outliers start: 54 outliers final: 28 residues processed: 170 average time/residue: 0.5555 time to fit residues: 106.1370 Evaluate side-chains 153 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain b residue 265 LEU Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain c residue 568 LEU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 378 CYS Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain d residue 492 GLU Chi-restraints excluded: chain e residue 648 GLU Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain g residue 626 MET Chi-restraints excluded: chain g residue 638 TYR Chi-restraints excluded: chain g residue 657 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 162 optimal weight: 0.0670 chunk 190 optimal weight: 5.9990 chunk 31 optimal weight: 0.0060 chunk 63 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 overall best weight: 0.9738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 616 ASN f 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.082572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.059018 restraints weight = 39777.164| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 4.10 r_work: 0.2749 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17788 Z= 0.128 Angle : 0.667 11.818 24371 Z= 0.299 Chirality : 0.045 0.286 3034 Planarity : 0.003 0.037 2869 Dihedral : 7.586 58.230 4764 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.72 % Favored : 97.23 % Rotamer: Outliers : 2.26 % Allowed : 15.51 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: 1915 helix: 0.51 (0.29), residues: 372 sheet: -0.17 (0.21), residues: 544 loop : -0.33 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG c 588 TYR 0.012 0.001 TYR L 49 PHE 0.010 0.001 PHE b 383 TRP 0.012 0.001 TRP f 338 HIS 0.011 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00296 (17622) covalent geometry : angle 0.60614 (23911) SS BOND : bond 0.00205 ( 38) SS BOND : angle 0.68084 ( 76) hydrogen bonds : bond 0.03927 ( 550) hydrogen bonds : angle 4.82805 ( 1524) link_ALPHA1-3 : bond 0.01101 ( 5) link_ALPHA1-3 : angle 2.44162 ( 15) link_ALPHA1-6 : bond 0.00490 ( 1) link_ALPHA1-6 : angle 1.36768 ( 3) link_BETA1-4 : bond 0.00588 ( 53) link_BETA1-4 : angle 2.85593 ( 159) link_NAG-ASN : bond 0.00241 ( 69) link_NAG-ASN : angle 1.73369 ( 207) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 71 SER cc_start: 0.8714 (t) cc_final: 0.8350 (p) REVERT: H 109 ASP cc_start: 0.7516 (t70) cc_final: 0.6895 (t70) REVERT: H 110 TYR cc_start: 0.6483 (OUTLIER) cc_final: 0.5970 (t80) REVERT: L 17 ASP cc_start: 0.8219 (m-30) cc_final: 0.7815 (m-30) REVERT: L 106 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8046 (mm-30) REVERT: b 187 ASN cc_start: 0.8382 (t0) cc_final: 0.7869 (t0) REVERT: c 530 MET cc_start: 0.7995 (mtt) cc_final: 0.7677 (mtt) REVERT: c 599 SER cc_start: 0.9058 (t) cc_final: 0.8724 (m) REVERT: c 621 GLU cc_start: 0.8811 (pt0) cc_final: 0.8545 (pp20) REVERT: c 647 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8134 (pm20) REVERT: d 475 MET cc_start: 0.8726 (tpp) cc_final: 0.8343 (tpp) REVERT: d 491 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8577 (tt) REVERT: d 492 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8369 (mm-30) REVERT: e 544 LEU cc_start: 0.9106 (mm) cc_final: 0.8888 (mm) REVERT: e 567 LYS cc_start: 0.8141 (mttt) cc_final: 0.7507 (mmtt) REVERT: e 588 ARG cc_start: 0.7969 (ttm-80) cc_final: 0.7713 (tmm-80) REVERT: f 322 ASP cc_start: 0.8605 (p0) cc_final: 0.8342 (p0) REVERT: g 567 LYS cc_start: 0.8123 (mmtm) cc_final: 0.7321 (tppp) REVERT: g 617 LYS cc_start: 0.9036 (mttm) cc_final: 0.8499 (mtpm) REVERT: g 657 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7384 (mt-10) outliers start: 39 outliers final: 21 residues processed: 157 average time/residue: 0.5815 time to fit residues: 102.0814 Evaluate side-chains 149 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 265 LEU Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain c residue 568 LEU Chi-restraints excluded: chain c residue 647 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 369 LEU Chi-restraints excluded: chain d residue 378 CYS Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain d residue 492 GLU Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain g residue 626 MET Chi-restraints excluded: chain g residue 638 TYR Chi-restraints excluded: chain g residue 657 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 151 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 127 optimal weight: 0.8980 chunk 189 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 195 ASN f 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.082397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.058893 restraints weight = 40284.848| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 4.07 r_work: 0.2765 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17788 Z= 0.118 Angle : 0.649 11.575 24371 Z= 0.291 Chirality : 0.044 0.269 3034 Planarity : 0.003 0.038 2869 Dihedral : 7.414 57.547 4764 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.37 % Allowed : 15.57 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: -0.15 (0.19), residues: 1915 helix: 0.59 (0.29), residues: 372 sheet: 0.02 (0.21), residues: 556 loop : -0.33 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG c 644 TYR 0.012 0.001 TYR L 49 PHE 0.008 0.001 PHE b 383 TRP 0.011 0.001 TRP f 338 HIS 0.003 0.001 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00267 (17622) covalent geometry : angle 0.58985 (23911) SS BOND : bond 0.00202 ( 38) SS BOND : angle 0.69881 ( 76) hydrogen bonds : bond 0.03712 ( 550) hydrogen bonds : angle 4.73827 ( 1524) link_ALPHA1-3 : bond 0.01069 ( 5) link_ALPHA1-3 : angle 2.37430 ( 15) link_ALPHA1-6 : bond 0.00552 ( 1) link_ALPHA1-6 : angle 1.40315 ( 3) link_BETA1-4 : bond 0.00592 ( 53) link_BETA1-4 : angle 2.78454 ( 159) link_NAG-ASN : bond 0.00239 ( 69) link_NAG-ASN : angle 1.66284 ( 207) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 71 SER cc_start: 0.8659 (t) cc_final: 0.8298 (p) REVERT: H 109 ASP cc_start: 0.7589 (t70) cc_final: 0.7258 (p0) REVERT: L 17 ASP cc_start: 0.8270 (m-30) cc_final: 0.7872 (m-30) REVERT: L 106 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8078 (mm-30) REVERT: b 42 VAL cc_start: 0.8287 (OUTLIER) cc_final: 0.7962 (m) REVERT: b 187 ASN cc_start: 0.8355 (t0) cc_final: 0.7818 (t0) REVERT: c 530 MET cc_start: 0.8110 (mtt) cc_final: 0.7764 (mtt) REVERT: c 599 SER cc_start: 0.9059 (t) cc_final: 0.8718 (m) REVERT: c 621 GLU cc_start: 0.8733 (pt0) cc_final: 0.8528 (pp20) REVERT: c 647 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8104 (pm20) REVERT: d 475 MET cc_start: 0.8766 (tpp) cc_final: 0.8378 (tpp) REVERT: e 567 LYS cc_start: 0.8169 (mttt) cc_final: 0.7521 (mmtt) REVERT: e 588 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7755 (tmm-80) REVERT: f 322 ASP cc_start: 0.8569 (p0) cc_final: 0.8345 (p0) REVERT: g 544 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8828 (mm) REVERT: g 567 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7354 (tppp) REVERT: g 584 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8480 (mt-10) REVERT: g 617 LYS cc_start: 0.9058 (mttm) cc_final: 0.8650 (mtpm) REVERT: g 626 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8572 (ttm) REVERT: g 656 ASN cc_start: 0.7778 (m-40) cc_final: 0.7506 (m-40) REVERT: g 657 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7296 (mt-10) outliers start: 41 outliers final: 25 residues processed: 161 average time/residue: 0.5880 time to fit residues: 106.3444 Evaluate side-chains 153 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 265 LEU Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain c residue 568 LEU Chi-restraints excluded: chain c residue 638 TYR Chi-restraints excluded: chain c residue 647 GLU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 369 LEU Chi-restraints excluded: chain d residue 378 CYS Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain g residue 544 LEU Chi-restraints excluded: chain g residue 626 MET Chi-restraints excluded: chain g residue 635 ILE Chi-restraints excluded: chain g residue 638 TYR Chi-restraints excluded: chain g residue 657 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 127 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 616 ASN f 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.082281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.058917 restraints weight = 40408.377| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 4.05 r_work: 0.2751 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17788 Z= 0.121 Angle : 0.652 11.141 24371 Z= 0.294 Chirality : 0.045 0.268 3034 Planarity : 0.003 0.038 2869 Dihedral : 7.364 57.379 4764 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.43 % Allowed : 15.57 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: -0.08 (0.19), residues: 1915 helix: 0.56 (0.29), residues: 375 sheet: 0.09 (0.22), residues: 520 loop : -0.27 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG e 644 TYR 0.013 0.001 TYR H 110 PHE 0.009 0.001 PHE b 383 TRP 0.011 0.001 TRP f 338 HIS 0.003 0.001 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00278 (17622) covalent geometry : angle 0.59537 (23911) SS BOND : bond 0.00196 ( 38) SS BOND : angle 0.66402 ( 76) hydrogen bonds : bond 0.03676 ( 550) hydrogen bonds : angle 4.71939 ( 1524) link_ALPHA1-3 : bond 0.01032 ( 5) link_ALPHA1-3 : angle 2.33887 ( 15) link_ALPHA1-6 : bond 0.00574 ( 1) link_ALPHA1-6 : angle 1.39627 ( 3) link_BETA1-4 : bond 0.00576 ( 53) link_BETA1-4 : angle 2.74430 ( 159) link_NAG-ASN : bond 0.00237 ( 69) link_NAG-ASN : angle 1.64550 ( 207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 71 SER cc_start: 0.8636 (t) cc_final: 0.8273 (p) REVERT: H 109 ASP cc_start: 0.7475 (t70) cc_final: 0.6937 (t0) REVERT: L 17 ASP cc_start: 0.8264 (m-30) cc_final: 0.7858 (m-30) REVERT: L 106 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8039 (mm-30) REVERT: b 42 VAL cc_start: 0.8291 (OUTLIER) cc_final: 0.7968 (m) REVERT: b 187 ASN cc_start: 0.8371 (t0) cc_final: 0.7850 (t0) REVERT: c 530 MET cc_start: 0.8172 (mtt) cc_final: 0.7833 (mtt) REVERT: c 599 SER cc_start: 0.9064 (t) cc_final: 0.8706 (m) REVERT: c 621 GLU cc_start: 0.8731 (pt0) cc_final: 0.8522 (pp20) REVERT: c 647 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8076 (pm20) REVERT: d 445 CYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7925 (p) REVERT: d 475 MET cc_start: 0.8767 (tpp) cc_final: 0.8376 (tpp) REVERT: e 567 LYS cc_start: 0.8144 (mttt) cc_final: 0.7480 (mmtt) REVERT: e 588 ARG cc_start: 0.8007 (ttm-80) cc_final: 0.7758 (tmm-80) REVERT: e 622 ILE cc_start: 0.7824 (mt) cc_final: 0.7416 (mp) REVERT: f 322 ASP cc_start: 0.8563 (p0) cc_final: 0.8341 (p0) REVERT: g 544 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8789 (mm) REVERT: g 567 LYS cc_start: 0.8115 (mmtm) cc_final: 0.7352 (tppp) REVERT: g 584 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8427 (mt-10) REVERT: g 617 LYS cc_start: 0.9065 (mttm) cc_final: 0.8571 (mtpm) REVERT: g 656 ASN cc_start: 0.7667 (m-40) cc_final: 0.7395 (m-40) REVERT: g 657 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7302 (mt-10) outliers start: 42 outliers final: 25 residues processed: 157 average time/residue: 0.5747 time to fit residues: 101.1237 Evaluate side-chains 153 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 265 LEU Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain c residue 638 TYR Chi-restraints excluded: chain c residue 647 GLU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 369 LEU Chi-restraints excluded: chain d residue 378 CYS Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain g residue 538 THR Chi-restraints excluded: chain g residue 544 LEU Chi-restraints excluded: chain g residue 638 TYR Chi-restraints excluded: chain g residue 657 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 14 optimal weight: 10.0000 chunk 24 optimal weight: 0.2980 chunk 147 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 162 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.081439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.057784 restraints weight = 40301.560| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 4.06 r_work: 0.2724 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17788 Z= 0.173 Angle : 0.681 11.213 24371 Z= 0.309 Chirality : 0.046 0.287 3034 Planarity : 0.003 0.047 2869 Dihedral : 7.515 58.572 4764 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.08 % Allowed : 15.97 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.22 (0.19), residues: 1915 helix: 0.46 (0.29), residues: 381 sheet: -0.05 (0.22), residues: 546 loop : -0.33 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG g 519 TYR 0.016 0.001 TYR e 643 PHE 0.012 0.001 PHE b 383 TRP 0.011 0.001 TRP f 338 HIS 0.004 0.001 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00413 (17622) covalent geometry : angle 0.62629 (23911) SS BOND : bond 0.00238 ( 38) SS BOND : angle 0.75306 ( 76) hydrogen bonds : bond 0.03961 ( 550) hydrogen bonds : angle 4.78560 ( 1524) link_ALPHA1-3 : bond 0.00860 ( 5) link_ALPHA1-3 : angle 2.29548 ( 15) link_ALPHA1-6 : bond 0.00455 ( 1) link_ALPHA1-6 : angle 1.31657 ( 3) link_BETA1-4 : bond 0.00552 ( 53) link_BETA1-4 : angle 2.74344 ( 159) link_NAG-ASN : bond 0.00275 ( 69) link_NAG-ASN : angle 1.71042 ( 207) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: H 14 LYS cc_start: 0.8763 (mtpm) cc_final: 0.8386 (mmtt) REVERT: H 71 SER cc_start: 0.8670 (t) cc_final: 0.8317 (p) REVERT: H 109 ASP cc_start: 0.7494 (t70) cc_final: 0.6879 (t0) REVERT: L 17 ASP cc_start: 0.8250 (m-30) cc_final: 0.7848 (m-30) REVERT: L 106 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8068 (mm-30) REVERT: b 42 VAL cc_start: 0.8324 (OUTLIER) cc_final: 0.8008 (m) REVERT: b 187 ASN cc_start: 0.8426 (t0) cc_final: 0.7921 (t0) REVERT: c 530 MET cc_start: 0.8189 (mtt) cc_final: 0.7844 (mtt) REVERT: c 599 SER cc_start: 0.9079 (t) cc_final: 0.8723 (m) REVERT: c 621 GLU cc_start: 0.8782 (pt0) cc_final: 0.8537 (pp20) REVERT: c 647 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8157 (pm20) REVERT: d 445 CYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7926 (p) REVERT: d 475 MET cc_start: 0.8756 (tpp) cc_final: 0.8378 (tpp) REVERT: d 491 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8759 (pt) REVERT: d 492 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8443 (mm-30) REVERT: e 588 ARG cc_start: 0.8047 (ttm-80) cc_final: 0.7791 (tmm-80) REVERT: f 322 ASP cc_start: 0.8603 (p0) cc_final: 0.8356 (p0) REVERT: g 544 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8842 (mm) REVERT: g 567 LYS cc_start: 0.8111 (mmtm) cc_final: 0.7347 (tppp) REVERT: g 617 LYS cc_start: 0.9080 (mttm) cc_final: 0.8666 (mtpm) REVERT: g 657 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7429 (mt-10) outliers start: 36 outliers final: 25 residues processed: 149 average time/residue: 0.5882 time to fit residues: 98.1642 Evaluate side-chains 151 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 265 LEU Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain c residue 638 TYR Chi-restraints excluded: chain c residue 647 GLU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 369 LEU Chi-restraints excluded: chain d residue 378 CYS Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain d residue 492 GLU Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain g residue 538 THR Chi-restraints excluded: chain g residue 544 LEU Chi-restraints excluded: chain g residue 657 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 111 optimal weight: 0.3980 chunk 92 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 616 ASN f 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.081215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.058405 restraints weight = 39949.885| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.97 r_work: 0.2737 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17788 Z= 0.144 Angle : 0.669 11.135 24371 Z= 0.303 Chirality : 0.045 0.282 3034 Planarity : 0.003 0.050 2869 Dihedral : 7.456 58.143 4764 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.14 % Allowed : 15.97 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: -0.13 (0.19), residues: 1915 helix: 0.72 (0.30), residues: 366 sheet: -0.07 (0.22), residues: 544 loop : -0.31 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG c 588 TYR 0.012 0.001 TYR L 49 PHE 0.010 0.001 PHE b 383 TRP 0.011 0.001 TRP f 338 HIS 0.003 0.001 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00338 (17622) covalent geometry : angle 0.61468 (23911) SS BOND : bond 0.00215 ( 38) SS BOND : angle 0.69211 ( 76) hydrogen bonds : bond 0.03848 ( 550) hydrogen bonds : angle 4.74625 ( 1524) link_ALPHA1-3 : bond 0.00891 ( 5) link_ALPHA1-3 : angle 2.27513 ( 15) link_ALPHA1-6 : bond 0.00511 ( 1) link_ALPHA1-6 : angle 1.33033 ( 3) link_BETA1-4 : bond 0.00561 ( 53) link_BETA1-4 : angle 2.71449 ( 159) link_NAG-ASN : bond 0.00242 ( 69) link_NAG-ASN : angle 1.65958 ( 207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4441.10 seconds wall clock time: 76 minutes 56.58 seconds (4616.58 seconds total)