Starting phenix.real_space_refine on Mon May 4 03:09:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nw0_49870/05_2026/9nw0_49870.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nw0_49870/05_2026/9nw0_49870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nw0_49870/05_2026/9nw0_49870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nw0_49870/05_2026/9nw0_49870.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nw0_49870/05_2026/9nw0_49870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nw0_49870/05_2026/9nw0_49870.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 10762 2.51 5 N 2836 2.21 5 O 3533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 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: 17241 Number of models: 1 Model: "" Number of chains: 54 Chain: "H" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1032 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "l" Number of atoms: 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: 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: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "v" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {'BMA': 1, 'MAN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "e" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "g" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.58, per 1000 atoms: 0.27 Number of scatterers: 17241 At special positions: 0 Unit cell: (134.46, 129.48, 154.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 3533 8.00 N 2836 7.00 C 10762 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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=2.04 Simple disulfide: pdb=" SG CYS b 385 " - pdb=" SG CYS b 418 " distance=2.03 Simple disulfide: pdb=" SG CYS b 501 " - pdb=" SG CYS c 605 " distance=2.03 Simple disulfide: pdb=" SG CYS c 598 " - pdb=" SG CYS c 604 " distance=2.03 Simple disulfide: pdb=" SG CYS d 54 " - pdb=" SG CYS d 74 " distance=2.03 Simple disulfide: pdb=" SG CYS d 119 " - pdb=" SG CYS d 205 " distance=2.05 Simple disulfide: pdb=" SG CYS d 126 " - pdb=" SG CYS d 196 " distance=2.02 Simple disulfide: pdb=" SG CYS d 131 " - pdb=" SG CYS d 157 " distance=2.03 Simple disulfide: pdb=" SG CYS d 201 " - pdb=" SG CYS d 433 " distance=2.03 Simple disulfide: pdb=" SG CYS d 218 " - pdb=" SG CYS d 247 " distance=2.03 Simple disulfide: pdb=" SG CYS d 228 " - pdb=" SG CYS d 239 " distance=2.03 Simple disulfide: pdb=" SG CYS d 296 " - pdb=" SG CYS d 331 " distance=2.03 Simple disulfide: pdb=" SG CYS d 378 " - pdb=" SG CYS d 445 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS e 598 " - pdb=" SG CYS e 604 " distance=2.03 Simple disulfide: pdb=" SG CYS f 54 " - pdb=" SG CYS f 74 " distance=2.04 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 205 " distance=2.03 Simple disulfide: pdb=" SG CYS f 126 " - pdb=" SG CYS f 196 " distance=2.03 Simple disulfide: pdb=" SG CYS f 131 " - pdb=" SG CYS f 157 " distance=2.03 Simple disulfide: pdb=" SG CYS f 201 " - pdb=" SG CYS f 433 " distance=2.03 Simple disulfide: pdb=" SG CYS f 218 " - pdb=" SG CYS f 247 " distance=2.03 Simple disulfide: pdb=" SG CYS f 228 " - pdb=" SG CYS f 239 " distance=2.03 Simple disulfide: pdb=" SG CYS f 296 " - pdb=" SG CYS f 331 " distance=2.03 Simple disulfide: pdb=" SG CYS f 378 " - pdb=" SG CYS f 445 " distance=2.04 Simple disulfide: pdb=" SG CYS f 385 " - pdb=" SG CYS f 418 " distance=2.03 Simple disulfide: pdb=" SG CYS f 501 " - pdb=" SG CYS g 605 " distance=2.03 Simple disulfide: pdb=" SG CYS g 598 " - pdb=" SG CYS g 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA R 3 " - " MAN R 4 " " BMA k 3 " - " MAN k 4 " " BMA u 3 " - " MAN u 4 " " BMA v 1 " - " MAN v 4 " ALPHA1-6 " BMA k 3 " - " MAN k 5 " " BMA u 3 " - " MAN u 5 " " BMA v 1 " - " MAN v 2 " " MAN v 2 " - " MAN v 3 " 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 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 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 d 392 " " NAG Q 1 " - " ASN d 332 " " NAG R 1 " - " ASN d 262 " " NAG S 1 " - " ASN d 156 " " NAG T 1 " - " ASN d 160 " " NAG U 1 " - " ASN d 197 " " NAG V 1 " - " ASN d 234 " " NAG W 1 " - " ASN d 241 " " NAG X 1 " - " ASN d 276 " " NAG Y 1 " - " ASN d 301 " " NAG Z 1 " - " ASN d 386 " " NAG a 1 " - " ASN d 448 " " NAG b 601 " - " ASN b 88 " " NAG b 602 " - " ASN b 133 " " NAG b 603 " - " ASN b 339 " " NAG b 604 " - " ASN b 355 " " NAG b 605 " - " ASN b 269 " " NAG b 606 " - " ASN b 398 " " NAG b 607 " - " ASN b 363 " " NAG c 701 " - " ASN c 611 " " NAG c 702 " - " ASN c 637 " " NAG c 703 " - " ASN c 625 " " NAG d 601 " - " ASN d 133 " " NAG d 602 " - " ASN d 355 " " NAG d 603 " - " ASN d 363 " " NAG d 604 " - " ASN d 269 " " NAG d 605 " - " ASN d 88 " " NAG d 606 " - " ASN d 398 " " NAG d 607 " - " ASN d 339 " " NAG e 701 " - " ASN e 611 " " NAG e 702 " - " ASN e 637 " " NAG e 703 " - " ASN e 625 " " NAG f 601 " - " ASN f 133 " " NAG f 602 " - " ASN f 339 " " NAG f 603 " - " ASN f 355 " " NAG f 604 " - " ASN f 269 " " NAG f 605 " - " ASN f 88 " " NAG f 606 " - " ASN f 398 " " NAG f 607 " - " ASN f 363 " " NAG g 701 " - " ASN g 611 " " NAG g 702 " - " ASN g 637 " " NAG g 703 " - " ASN g 625 " " NAG h 1 " - " ASN d 465 " " NAG i 1 " - " ASN f 392 " " NAG j 1 " - " ASN f 332 " " NAG k 1 " - " ASN f 262 " " NAG l 1 " - " ASN f 156 " " NAG m 1 " - " ASN f 197 " " NAG n 1 " - " ASN f 234 " " NAG o 1 " - " ASN f 241 " " NAG p 1 " - " ASN f 276 " " NAG q 1 " - " ASN f 301 " " NAG r 1 " - " ASN f 386 " " NAG s 1 " - " ASN f 448 " " NAG t 1 " - " ASN f 465 " " NAG u 1 " - " ASN f 160 " Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 713.1 milliseconds 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3640 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 32 sheets defined 22.8% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.766A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.895A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'b' and resid 98 through 117 removed outlier: 4.188A pdb=" N GLU b 102 " --> pdb=" O ASN b 98 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 126 removed outlier: 3.512A pdb=" N LEU b 125 " --> pdb=" O LEU b 122 " (cutoff:3.500A) removed outlier: 3.572A 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 351 removed outlier: 3.956A pdb=" N THR b 341 " --> pdb=" O ARG b 337 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU b 342 " --> pdb=" O TRP b 338 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR b 351 " --> pdb=" O GLU b 347 " (cutoff:3.500A) Processing helix chain 'b' and resid 387 through 390 Processing helix chain 'b' and resid 475 through 484 removed outlier: 3.982A pdb=" N TRP b 479 " --> pdb=" O MET b 475 " (cutoff:3.500A) removed outlier: 3.974A 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 543 removed outlier: 3.783A pdb=" N GLN c 540 " --> pdb=" O THR c 536 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN c 543 " --> pdb=" O VAL c 539 " (cutoff:3.500A) Processing helix chain 'c' and resid 569 through 596 removed outlier: 3.876A pdb=" N LEU c 592 " --> pdb=" O ARG c 588 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU c 593 " --> pdb=" O ASP c 589 " (cutoff:3.500A) Processing helix chain 'c' and resid 618 through 625 Processing helix chain 'c' and resid 627 through 636 removed outlier: 3.619A pdb=" N LYS c 633 " --> pdb=" O LEU c 629 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU c 634 " --> pdb=" O GLN c 630 " (cutoff:3.500A) Processing helix chain 'c' and resid 638 through 658 Processing helix chain 'd' and resid 98 through 117 removed outlier: 3.985A pdb=" N GLU d 102 " --> pdb=" O ASN d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 334 through 351 removed outlier: 3.623A pdb=" N LYS d 340 " --> pdb=" O SER d 336 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR d 341 " --> pdb=" O ARG d 337 " (cutoff:3.500A) removed outlier: 3.555A 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: 4.133A pdb=" N TRP d 479 " --> pdb=" O MET d 475 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU d 482 " --> pdb=" O ASN d 478 " (cutoff:3.500A) Processing helix chain 'e' and resid 523 through 527 removed outlier: 3.567A pdb=" N ALA e 526 " --> pdb=" O LEU e 523 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY e 527 " --> pdb=" O GLY e 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 523 through 527' Processing helix chain 'e' and resid 529 through 534 Processing helix chain 'e' and resid 536 through 543 removed outlier: 3.849A pdb=" N GLN e 540 " --> pdb=" O THR e 536 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN e 543 " --> pdb=" O VAL e 539 " (cutoff:3.500A) Processing helix chain 'e' and resid 544 through 546 No H-bonds generated for 'chain 'e' and resid 544 through 546' Processing helix chain 'e' and resid 569 through 596 removed outlier: 3.597A pdb=" N LYS e 574 " --> pdb=" O VAL e 570 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU e 592 " --> pdb=" O ARG e 588 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU e 593 " --> pdb=" O ASP e 589 " (cutoff:3.500A) Processing helix chain 'e' and resid 618 through 624 Processing helix chain 'e' and resid 627 through 658 removed outlier: 3.837A pdb=" N LYS e 633 " --> pdb=" O LEU e 629 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU e 634 " --> pdb=" O GLN e 630 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE e 635 " --> pdb=" O TRP e 631 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ASN e 637 " --> pdb=" O LYS e 633 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N TYR e 638 " --> pdb=" O GLU e 634 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLN e 640 " --> pdb=" O GLY e 636 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU e 641 " --> pdb=" O ASN e 637 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU e 647 " --> pdb=" O TYR e 643 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU e 648 " --> pdb=" O ARG e 644 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER e 649 " --> pdb=" O LEU e 645 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 74 Processing helix chain 'f' and resid 98 through 117 removed outlier: 4.264A pdb=" N GLU f 102 " --> pdb=" O ASN f 98 " (cutoff:3.500A) Processing helix chain 'f' and resid 122 through 126 removed outlier: 3.541A pdb=" N LEU f 125 " --> pdb=" O LEU f 122 " (cutoff:3.500A) removed outlier: 3.649A 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 335 through 351 removed outlier: 3.558A pdb=" N THR f 351 " --> pdb=" O GLU f 347 " (cutoff:3.500A) Processing helix chain 'f' and resid 368 through 373 Processing helix chain 'f' and resid 387 through 390 Processing helix chain 'f' and resid 475 through 484 removed outlier: 4.163A pdb=" N TRP f 479 " --> pdb=" O MET f 475 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU f 482 " --> pdb=" O ASN f 478 " (cutoff:3.500A) Processing helix chain 'g' and resid 529 through 534 Processing helix chain 'g' and resid 536 through 543 removed outlier: 3.727A pdb=" N GLN g 540 " --> pdb=" O THR g 536 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN g 543 " --> pdb=" O VAL g 539 " (cutoff:3.500A) Processing helix chain 'g' and resid 544 through 546 No H-bonds generated for 'chain 'g' and resid 544 through 546' Processing helix chain 'g' and resid 569 through 596 removed outlier: 3.815A pdb=" N LEU g 592 " --> pdb=" O ARG g 588 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU g 593 " --> pdb=" O ASP g 589 " (cutoff:3.500A) Processing helix chain 'g' and resid 618 through 625 removed outlier: 3.558A pdb=" N ILE g 622 " --> pdb=" O SER g 618 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP g 623 " --> pdb=" O LEU g 619 " (cutoff:3.500A) Processing helix chain 'g' and resid 627 through 636 removed outlier: 3.826A pdb=" N LYS g 633 " --> pdb=" O LEU g 629 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU g 634 " --> pdb=" O GLN g 630 " (cutoff:3.500A) Processing helix chain 'g' and resid 638 through 658 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.594A pdb=" N LEU H 18 " --> pdb=" O TRP H 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.589A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.754A pdb=" N CYS H 96 " --> pdb=" O TRP H 121 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TRP H 121 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS H 98 " --> pdb=" O ASP H 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 103 through 105 removed outlier: 6.504A pdb=" N TYR H 111 " --> pdb=" O ARG f 169 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LYS f 171 " --> pdb=" O TYR H 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.528A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.047A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 494 through 499 removed outlier: 5.389A pdb=" N VAL c 608 " --> pdb=" O VAL b 36 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL b 38 " --> pdb=" O THR c 606 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR c 606 " --> pdb=" O VAL b 38 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TYR b 40 " --> pdb=" O CYS c 604 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N CYS c 604 " --> pdb=" O TYR b 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 45 through 47 removed outlier: 4.708A pdb=" N VAL b 242 " --> pdb=" O LEU b 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 53 through 55 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: 6.291A 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: 6.347A pdb=" N LEU b 260 " --> pdb=" O THR b 450 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N LYS b 444 " --> pdb=" O ILE b 294 " (cutoff:3.500A) removed outlier: 11.387A pdb=" N ILE b 294 " --> pdb=" O LYS b 444 " (cutoff:3.500A) removed outlier: 9.699A pdb=" N GLU b 446 " --> pdb=" O VAL b 292 " (cutoff:3.500A) removed outlier: 10.615A pdb=" N VAL b 292 " --> pdb=" O GLU b 446 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N ASN b 448 " --> pdb=" O GLN b 290 " (cutoff:3.500A) removed outlier: 9.927A pdb=" N GLN b 290 " --> pdb=" O ASN b 448 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR b 450 " --> pdb=" O LEU b 288 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS b 330 " --> pdb=" O ILE b 297 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA b 329 " --> pdb=" O CYS b 418 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS b 421 " --> pdb=" O PHE b 382 " (cutoff:3.500A) removed outlier: 4.564A 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: 6.572A pdb=" N THR b 450 " --> pdb=" O LEU b 288 " (cutoff:3.500A) removed outlier: 9.927A pdb=" N GLN b 290 " --> pdb=" O ASN b 448 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N ASN b 448 " --> pdb=" O GLN b 290 " (cutoff:3.500A) removed outlier: 10.615A pdb=" N VAL b 292 " --> pdb=" O GLU b 446 " (cutoff:3.500A) removed outlier: 9.699A pdb=" N GLU b 446 " --> pdb=" O VAL b 292 " (cutoff:3.500A) removed outlier: 11.387A pdb=" N ILE b 294 " --> pdb=" O LYS b 444 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N LYS b 444 " --> pdb=" O ILE b 294 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR b 357 " --> pdb=" O GLU b 466 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N PHE b 468 " --> pdb=" O THR b 357 " (cutoff:3.500A) removed outlier: 6.744A 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: 6.419A pdb=" N THR b 303 " --> pdb=" O GLY b 321 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLN b 315 " --> pdb=" O ILE b 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'd' and resid 495 through 499 removed outlier: 5.431A pdb=" N VAL e 608 " --> pdb=" O VAL d 36 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N VAL d 38 " --> pdb=" O THR e 606 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N THR e 606 " --> pdb=" O VAL d 38 " (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 53 through 55 Processing sheet with id=AC1, first strand: chain 'd' and resid 66 through 67 removed outlier: 7.285A pdb=" N HIS d 66 " --> pdb=" O SER d 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'd' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'd' and resid 169 through 177 Processing sheet with id=AC4, first strand: chain 'd' and resid 202 through 203 removed outlier: 6.422A pdb=" N THR d 202 " --> pdb=" O TYR d 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'd' and resid 259 through 261 removed outlier: 3.562A pdb=" N GLY d 451 " --> pdb=" O LEU d 260 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N LYS d 444 " --> pdb=" O ILE d 294 " (cutoff:3.500A) removed outlier: 11.343A pdb=" N ILE d 294 " --> pdb=" O LYS d 444 " (cutoff:3.500A) removed outlier: 9.713A pdb=" N GLU d 446 " --> pdb=" O VAL d 292 " (cutoff:3.500A) removed outlier: 10.565A pdb=" N VAL d 292 " --> pdb=" O GLU d 446 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N ASN d 448 " --> pdb=" O GLN d 290 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N GLN d 290 " --> pdb=" O ASN d 448 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR d 450 " --> pdb=" O LEU d 288 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS d 330 " --> pdb=" O ILE d 297 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA d 329 " --> pdb=" O CYS d 418 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS d 421 " --> pdb=" O PHE d 382 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N PHE d 382 " --> pdb=" O LYS d 421 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'd' and resid 271 through 273 removed outlier: 6.407A pdb=" N THR d 450 " --> pdb=" O LEU d 288 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N GLN d 290 " --> pdb=" O ASN d 448 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N ASN d 448 " --> pdb=" O GLN d 290 " (cutoff:3.500A) removed outlier: 10.565A pdb=" N VAL d 292 " --> pdb=" O GLU d 446 " (cutoff:3.500A) removed outlier: 9.713A pdb=" N GLU d 446 " --> pdb=" O VAL d 292 " (cutoff:3.500A) removed outlier: 11.343A pdb=" N ILE d 294 " --> pdb=" O LYS d 444 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N LYS d 444 " --> pdb=" O ILE d 294 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR d 357 " --> pdb=" O GLU d 466 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE d 468 " --> pdb=" O THR d 357 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE d 359 " --> pdb=" O PHE d 468 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'd' and resid 302 through 312 removed outlier: 6.472A pdb=" N THR d 303 " --> pdb=" O GLY d 321 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLN d 315 " --> pdb=" O ILE d 309 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'f' and resid 495 through 499 removed outlier: 5.339A pdb=" N VAL g 608 " --> pdb=" O VAL f 36 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL f 38 " --> pdb=" O THR g 606 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N THR g 606 " --> pdb=" O VAL f 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'f' and resid 45 through 47 Processing sheet with id=AD1, first strand: chain 'f' and resid 91 through 94 Processing sheet with id=AD2, first strand: chain 'f' and resid 202 through 203 removed outlier: 6.161A pdb=" N THR f 202 " --> pdb=" O TYR f 435 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'f' and resid 259 through 261 removed outlier: 3.506A pdb=" N GLY f 451 " --> pdb=" O LEU f 260 " (cutoff:3.500A) removed outlier: 10.108A pdb=" N LYS f 444 " --> pdb=" O ILE f 294 " (cutoff:3.500A) removed outlier: 11.495A pdb=" N ILE f 294 " --> pdb=" O LYS f 444 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N GLU f 446 " --> pdb=" O VAL f 292 " (cutoff:3.500A) removed outlier: 10.627A pdb=" N VAL f 292 " --> pdb=" O GLU f 446 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ASN f 448 " --> pdb=" O GLN f 290 " (cutoff:3.500A) removed outlier: 9.866A pdb=" N GLN f 290 " --> pdb=" O ASN f 448 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR f 450 " --> pdb=" O LEU f 288 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR f 293 " --> pdb=" O SER f 334 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER f 334 " --> pdb=" O THR f 293 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS f 330 " --> pdb=" O ILE f 297 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA f 329 " --> pdb=" O CYS f 418 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS f 421 " --> pdb=" O PHE f 382 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE f 382 " --> pdb=" O LYS f 421 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'f' and resid 271 through 273 removed outlier: 6.651A pdb=" N THR f 450 " --> pdb=" O LEU f 288 " (cutoff:3.500A) removed outlier: 9.866A pdb=" N GLN f 290 " --> pdb=" O ASN f 448 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ASN f 448 " --> pdb=" O GLN f 290 " (cutoff:3.500A) removed outlier: 10.627A pdb=" N VAL f 292 " --> pdb=" O GLU f 446 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N GLU f 446 " --> pdb=" O VAL f 292 " (cutoff:3.500A) removed outlier: 11.495A pdb=" N ILE f 294 " --> pdb=" O LYS f 444 " (cutoff:3.500A) removed outlier: 10.108A pdb=" N LYS f 444 " --> pdb=" O ILE f 294 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR f 357 " --> pdb=" O GLU f 466 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N PHE f 468 " --> pdb=" O THR f 357 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE f 359 " --> pdb=" O PHE f 468 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'f' and resid 302 through 312 removed outlier: 6.492A pdb=" N THR f 303 " --> pdb=" O GLY f 321 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLN f 315 " --> pdb=" O ILE f 309 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1557 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 2659 1.28 - 1.42: 4722 1.42 - 1.56: 10047 1.56 - 1.70: 4 1.70 - 1.84: 142 Bond restraints: 17574 Sorted by residual: bond pdb=" C LEU d 86 " pdb=" O LEU d 86 " ideal model delta sigma weight residual 1.234 1.138 0.096 1.24e-02 6.50e+03 6.01e+01 bond pdb=" CA SER b 189 " pdb=" CB SER b 189 " ideal model delta sigma weight residual 1.539 1.477 0.061 1.20e-02 6.94e+03 2.62e+01 bond pdb=" C5 NAG b 607 " pdb=" O5 NAG b 607 " ideal model delta sigma weight residual 1.413 1.492 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" N ILE b 371 " pdb=" CA ILE b 371 " ideal model delta sigma weight residual 1.456 1.492 -0.035 9.50e-03 1.11e+04 1.38e+01 bond pdb=" C5 NAG b 606 " pdb=" O5 NAG b 606 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 17569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 23407 3.25 - 6.50: 414 6.50 - 9.75: 16 9.75 - 13.01: 3 13.01 - 16.26: 1 Bond angle restraints: 23841 Sorted by residual: angle pdb=" N PHE H 29 " pdb=" CA PHE H 29 " pdb=" CB PHE H 29 " ideal model delta sigma weight residual 110.49 94.23 16.26 1.69e+00 3.50e-01 9.25e+01 angle pdb=" C ASP f 87 " pdb=" N ASN f 88 " pdb=" CA ASN f 88 " ideal model delta sigma weight residual 123.05 134.33 -11.28 1.57e+00 4.06e-01 5.16e+01 angle pdb=" N ASN b 187 " pdb=" CA ASN b 187 " pdb=" C ASN b 187 " ideal model delta sigma weight residual 112.89 104.72 8.17 1.24e+00 6.50e-01 4.34e+01 angle pdb=" CA ASP f 87 " pdb=" C ASP f 87 " pdb=" O ASP f 87 " ideal model delta sigma weight residual 121.55 115.17 6.38 1.06e+00 8.90e-01 3.62e+01 angle pdb=" CA ASP f 87 " pdb=" C ASP f 87 " pdb=" N ASN f 88 " ideal model delta sigma weight residual 115.56 123.19 -7.63 1.30e+00 5.92e-01 3.45e+01 ... (remaining 23836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.93: 11642 25.93 - 51.85: 416 51.85 - 77.78: 81 77.78 - 103.70: 43 103.70 - 129.63: 17 Dihedral angle restraints: 12199 sinusoidal: 6559 harmonic: 5640 Sorted by residual: dihedral pdb=" CB CYS d 119 " pdb=" SG CYS d 119 " pdb=" SG CYS d 205 " pdb=" CB CYS d 205 " ideal model delta sinusoidal sigma weight residual -86.00 -6.74 -79.26 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CB CYS d 126 " pdb=" SG CYS d 126 " pdb=" SG CYS d 196 " pdb=" CB CYS d 196 " ideal model delta sinusoidal sigma weight residual 93.00 157.05 -64.05 1 1.00e+01 1.00e-02 5.40e+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 93.00 154.15 -61.15 1 1.00e+01 1.00e-02 4.97e+01 ... (remaining 12196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2886 0.123 - 0.245: 122 0.245 - 0.368: 4 0.368 - 0.490: 3 0.490 - 0.613: 4 Chirality restraints: 3019 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 -2.17 -0.23 2.00e-02 2.50e+03 1.28e+02 chirality pdb=" C1 NAG k 2 " pdb=" O4 NAG k 1 " pdb=" C2 NAG k 2 " pdb=" O5 NAG k 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.60e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.21e+01 ... (remaining 3016 not shown) Planarity restraints: 2925 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 605 " -0.292 2.00e-02 2.50e+03 2.54e-01 8.07e+02 pdb=" C7 NAG f 605 " 0.061 2.00e-02 2.50e+03 pdb=" C8 NAG f 605 " -0.022 2.00e-02 2.50e+03 pdb=" N2 NAG f 605 " 0.444 2.00e-02 2.50e+03 pdb=" O7 NAG f 605 " -0.191 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 605 " -0.216 2.00e-02 2.50e+03 1.81e-01 4.08e+02 pdb=" C7 NAG d 605 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG d 605 " -0.150 2.00e-02 2.50e+03 pdb=" N2 NAG d 605 " 0.301 2.00e-02 2.50e+03 pdb=" O7 NAG d 605 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 606 " 0.189 2.00e-02 2.50e+03 1.64e-01 3.35e+02 pdb=" C7 NAG f 606 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG f 606 " -0.021 2.00e-02 2.50e+03 pdb=" N2 NAG f 606 " -0.274 2.00e-02 2.50e+03 pdb=" O7 NAG f 606 " 0.145 2.00e-02 2.50e+03 ... (remaining 2922 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 126 2.59 - 3.17: 14752 3.17 - 3.75: 25035 3.75 - 4.32: 35850 4.32 - 4.90: 60336 Nonbonded interactions: 136099 Sorted by model distance: nonbonded pdb=" O ILE d 194 " pdb=" OD1 ASN d 195 " model vdw 2.017 3.040 nonbonded pdb=" O TRP b 401 " pdb=" O3 NAG b 603 " model vdw 2.054 3.040 nonbonded pdb=" OG1 THR b 303 " pdb=" OD1 ASP b 322 " model vdw 2.107 3.040 nonbonded pdb=" OG1 THR d 303 " pdb=" OD1 ASP d 322 " model vdw 2.115 3.040 nonbonded pdb=" OG1 THR f 303 " pdb=" OD1 ASP f 322 " model vdw 2.130 3.040 ... (remaining 136094 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 'E' 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 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'h' selection = chain 'i' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'Q' selection = chain 'j' selection = chain 'o' } ncs_group { reference = (chain 'C' and resid 4) selection = (chain 'R' and resid 4) selection = (chain 'v' and resid 4) } ncs_group { reference = chain 'b' selection = chain 'd' selection = chain 'f' } ncs_group { reference = chain 'c' selection = chain 'e' selection = chain 'g' } ncs_group { reference = chain 'k' selection = chain 'u' } 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: 3.680 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.250 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 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 0.115 17738 Z= 0.323 Angle : 1.111 24.097 24295 Z= 0.579 Chirality : 0.059 0.613 3019 Planarity : 0.009 0.254 2856 Dihedral : 14.646 129.629 8445 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Cbeta Deviations : 0.16 % 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: -1.20 (0.18), residues: 1910 helix: -0.71 (0.26), residues: 402 sheet: -0.72 (0.23), residues: 474 loop : -0.76 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG f 169 TYR 0.073 0.002 TYR b 396 PHE 0.036 0.002 PHE b 353 TRP 0.060 0.002 TRP b 395 HIS 0.005 0.001 HIS e 564 Details of bonding type rmsd covalent geometry : bond 0.00554 (17574) covalent geometry : angle 0.96339 (23841) SS BOND : bond 0.00459 ( 38) SS BOND : angle 1.81763 ( 76) hydrogen bonds : bond 0.22818 ( 554) hydrogen bonds : angle 8.40778 ( 1557) link_ALPHA1-3 : bond 0.02625 ( 5) link_ALPHA1-3 : angle 1.99808 ( 15) link_ALPHA1-6 : bond 0.01279 ( 4) link_ALPHA1-6 : angle 2.27332 ( 12) link_BETA1-4 : bond 0.02151 ( 48) link_BETA1-4 : angle 4.33340 ( 144) link_NAG-ASN : bond 0.02825 ( 69) link_NAG-ASN : angle 4.79886 ( 207) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 80 TYR cc_start: 0.8182 (m-80) cc_final: 0.7938 (m-80) REVERT: H 86 LEU cc_start: 0.8497 (mp) cc_final: 0.8183 (mp) REVERT: L 79 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7974 (mm-40) REVERT: c 536 THR cc_start: 0.9103 (p) cc_final: 0.8871 (t) REVERT: c 633 LYS cc_start: 0.8539 (ptpp) cc_final: 0.8281 (mttt) REVERT: e 639 THR cc_start: 0.8729 (m) cc_final: 0.8439 (p) REVERT: g 567 LYS cc_start: 0.8777 (mmpt) cc_final: 0.8015 (pttt) REVERT: g 644 ARG cc_start: 0.8616 (mmt-90) cc_final: 0.8002 (mmt-90) REVERT: g 657 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7458 (mp0) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.7574 time to fit residues: 146.5797 Evaluate side-chains 110 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 187 ASN e 607 ASN f 130 HIS g 616 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.078439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.061024 restraints weight = 50458.520| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.73 r_work: 0.3088 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17738 Z= 0.175 Angle : 0.773 17.164 24295 Z= 0.350 Chirality : 0.048 0.335 3019 Planarity : 0.004 0.041 2856 Dihedral : 10.495 110.999 4729 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.85 % Allowed : 11.23 % Favored : 86.91 % 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: -0.74 (0.18), residues: 1910 helix: 0.05 (0.27), residues: 390 sheet: -0.52 (0.22), residues: 497 loop : -0.59 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG f 46 TYR 0.014 0.001 TYR H 95 PHE 0.018 0.002 PHE H 29 TRP 0.023 0.002 TRP H 83 HIS 0.004 0.001 HIS H 67 Details of bonding type rmsd covalent geometry : bond 0.00411 (17574) covalent geometry : angle 0.68998 (23841) SS BOND : bond 0.00317 ( 38) SS BOND : angle 1.10261 ( 76) hydrogen bonds : bond 0.04472 ( 554) hydrogen bonds : angle 5.90641 ( 1557) link_ALPHA1-3 : bond 0.01039 ( 5) link_ALPHA1-3 : angle 2.04305 ( 15) link_ALPHA1-6 : bond 0.00668 ( 4) link_ALPHA1-6 : angle 2.15643 ( 12) link_BETA1-4 : bond 0.00602 ( 48) link_BETA1-4 : angle 3.07547 ( 144) link_NAG-ASN : bond 0.00364 ( 69) link_NAG-ASN : angle 2.77275 ( 207) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 45 LYS cc_start: 0.8959 (ttmm) cc_final: 0.8606 (tttp) REVERT: L 79 GLN cc_start: 0.8394 (mm-40) cc_final: 0.8103 (mm-40) REVERT: b 434 MET cc_start: 0.8668 (ttp) cc_final: 0.8465 (ttp) REVERT: c 536 THR cc_start: 0.9220 (p) cc_final: 0.8951 (t) REVERT: c 588 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7825 (ttm170) REVERT: d 475 MET cc_start: 0.8802 (tpp) cc_final: 0.8601 (tpp) REVERT: e 639 THR cc_start: 0.8578 (m) cc_final: 0.8271 (p) REVERT: e 657 GLU cc_start: 0.8070 (tp30) cc_final: 0.7505 (mm-30) REVERT: g 656 ASN cc_start: 0.8922 (m-40) cc_final: 0.8671 (m-40) outliers start: 32 outliers final: 15 residues processed: 149 average time/residue: 0.6345 time to fit residues: 105.3585 Evaluate side-chains 122 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain c residue 588 ARG Chi-restraints excluded: chain c residue 620 ASP Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 119 CYS Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain e residue 546 SER Chi-restraints excluded: chain e residue 599 SER Chi-restraints excluded: chain e residue 612 SER Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 103 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 195 ASN d 195 ASN d 330 HIS e 651 ASN f 330 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.077187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.059688 restraints weight = 51016.554| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.74 r_work: 0.3048 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17738 Z= 0.193 Angle : 0.735 17.587 24295 Z= 0.333 Chirality : 0.047 0.273 3019 Planarity : 0.004 0.037 2856 Dihedral : 9.543 108.614 4729 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.84 % Allowed : 11.99 % Favored : 85.18 % 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: -0.44 (0.19), residues: 1910 helix: 0.32 (0.28), residues: 387 sheet: -0.26 (0.22), residues: 496 loop : -0.45 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG g 519 TYR 0.016 0.001 TYR c 638 PHE 0.014 0.001 PHE b 383 TRP 0.014 0.001 TRP c 623 HIS 0.004 0.001 HIS f 130 Details of bonding type rmsd covalent geometry : bond 0.00464 (17574) covalent geometry : angle 0.65325 (23841) SS BOND : bond 0.00346 ( 38) SS BOND : angle 1.39895 ( 76) hydrogen bonds : bond 0.04311 ( 554) hydrogen bonds : angle 5.51912 ( 1557) link_ALPHA1-3 : bond 0.01035 ( 5) link_ALPHA1-3 : angle 1.82871 ( 15) link_ALPHA1-6 : bond 0.00571 ( 4) link_ALPHA1-6 : angle 2.07149 ( 12) link_BETA1-4 : bond 0.00569 ( 48) link_BETA1-4 : angle 2.86029 ( 144) link_NAG-ASN : bond 0.00328 ( 69) link_NAG-ASN : angle 2.71601 ( 207) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 121 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 45 LYS cc_start: 0.8974 (ttmm) cc_final: 0.8601 (tttp) REVERT: L 79 GLN cc_start: 0.8388 (mm-40) cc_final: 0.7990 (mm110) REVERT: c 536 THR cc_start: 0.9265 (p) cc_final: 0.8986 (t) REVERT: c 588 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7834 (ttm170) REVERT: c 601 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8298 (mtpp) REVERT: c 621 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8295 (pp20) REVERT: c 644 ARG cc_start: 0.8959 (mmp80) cc_final: 0.8702 (mmp80) REVERT: e 639 THR cc_start: 0.8624 (m) cc_final: 0.8278 (p) REVERT: e 657 GLU cc_start: 0.8081 (tp30) cc_final: 0.7552 (mm-30) REVERT: g 656 ASN cc_start: 0.8923 (m-40) cc_final: 0.8668 (m-40) outliers start: 49 outliers final: 30 residues processed: 160 average time/residue: 0.5811 time to fit residues: 104.5998 Evaluate side-chains 139 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 452 LEU Chi-restraints excluded: chain b residue 467 THR Chi-restraints excluded: chain c residue 588 ARG Chi-restraints excluded: chain c residue 601 LYS Chi-restraints excluded: chain c residue 620 ASP Chi-restraints excluded: chain c residue 621 GLU Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain c residue 654 GLU Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 119 CYS Chi-restraints excluded: chain d residue 195 ASN Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain e residue 546 SER Chi-restraints excluded: chain e residue 599 SER Chi-restraints excluded: chain e residue 604 CYS Chi-restraints excluded: chain e residue 612 SER Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 51 THR Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 488 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 154 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 67 HIS ** b 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 651 ASN d 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.077166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.059858 restraints weight = 50849.677| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.70 r_work: 0.3037 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17738 Z= 0.164 Angle : 0.708 17.434 24295 Z= 0.321 Chirality : 0.046 0.272 3019 Planarity : 0.003 0.035 2856 Dihedral : 9.166 107.111 4729 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.01 % Allowed : 12.91 % Favored : 84.08 % 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: 1910 helix: 0.67 (0.29), residues: 369 sheet: -0.23 (0.22), residues: 495 loop : -0.44 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG e 644 TYR 0.015 0.001 TYR c 638 PHE 0.013 0.001 PHE b 383 TRP 0.012 0.001 TRP b 96 HIS 0.004 0.001 HIS f 130 Details of bonding type rmsd covalent geometry : bond 0.00391 (17574) covalent geometry : angle 0.62892 (23841) SS BOND : bond 0.00312 ( 38) SS BOND : angle 1.30278 ( 76) hydrogen bonds : bond 0.03856 ( 554) hydrogen bonds : angle 5.36332 ( 1557) link_ALPHA1-3 : bond 0.01070 ( 5) link_ALPHA1-3 : angle 1.95470 ( 15) link_ALPHA1-6 : bond 0.00693 ( 4) link_ALPHA1-6 : angle 2.02301 ( 12) link_BETA1-4 : bond 0.00564 ( 48) link_BETA1-4 : angle 2.75553 ( 144) link_NAG-ASN : bond 0.00302 ( 69) link_NAG-ASN : angle 2.63337 ( 207) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 120 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 40 MET cc_start: 0.8826 (mmm) cc_final: 0.8571 (mpt) REVERT: L 45 LYS cc_start: 0.8989 (ttmm) cc_final: 0.8631 (tttp) REVERT: L 79 GLN cc_start: 0.8406 (mm-40) cc_final: 0.7977 (mm110) REVERT: c 536 THR cc_start: 0.9266 (p) cc_final: 0.8990 (t) REVERT: c 601 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8308 (mtpp) REVERT: c 621 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8375 (pp20) REVERT: e 639 THR cc_start: 0.8569 (m) cc_final: 0.8250 (p) REVERT: g 656 ASN cc_start: 0.8886 (m-40) cc_final: 0.8618 (m-40) outliers start: 52 outliers final: 27 residues processed: 164 average time/residue: 0.6108 time to fit residues: 111.7394 Evaluate side-chains 132 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 134 VAL Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 452 LEU Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain c residue 601 LYS Chi-restraints excluded: chain c residue 621 GLU Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain c residue 654 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 119 CYS Chi-restraints excluded: chain d residue 195 ASN Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain e residue 546 SER Chi-restraints excluded: chain e residue 599 SER Chi-restraints excluded: chain e residue 604 CYS Chi-restraints excluded: chain e residue 612 SER Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 51 THR Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 488 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 83 optimal weight: 7.9990 chunk 187 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 67 HIS d 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.077019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.059568 restraints weight = 50585.208| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.72 r_work: 0.3030 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17738 Z= 0.166 Angle : 0.704 17.397 24295 Z= 0.317 Chirality : 0.046 0.275 3019 Planarity : 0.003 0.036 2856 Dihedral : 8.948 105.708 4729 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.90 % Allowed : 13.49 % Favored : 83.61 % 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: -0.28 (0.19), residues: 1910 helix: 0.46 (0.28), residues: 387 sheet: -0.03 (0.23), residues: 465 loop : -0.43 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG c 644 TYR 0.015 0.001 TYR c 638 PHE 0.012 0.001 PHE b 383 TRP 0.012 0.001 TRP b 96 HIS 0.004 0.001 HIS f 130 Details of bonding type rmsd covalent geometry : bond 0.00398 (17574) covalent geometry : angle 0.62742 (23841) SS BOND : bond 0.00398 ( 38) SS BOND : angle 1.23948 ( 76) hydrogen bonds : bond 0.03797 ( 554) hydrogen bonds : angle 5.28850 ( 1557) link_ALPHA1-3 : bond 0.01033 ( 5) link_ALPHA1-3 : angle 1.94273 ( 15) link_ALPHA1-6 : bond 0.00742 ( 4) link_ALPHA1-6 : angle 2.02791 ( 12) link_BETA1-4 : bond 0.00568 ( 48) link_BETA1-4 : angle 2.69054 ( 144) link_NAG-ASN : bond 0.00300 ( 69) link_NAG-ASN : angle 2.60166 ( 207) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 114 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 16 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8037 (pm20) REVERT: H 23 LYS cc_start: 0.7552 (mmmm) cc_final: 0.7323 (mmmm) REVERT: H 40 MET cc_start: 0.8874 (mmm) cc_final: 0.8672 (mpt) REVERT: L 45 LYS cc_start: 0.9000 (ttmm) cc_final: 0.8652 (tttp) REVERT: L 79 GLN cc_start: 0.8388 (mm-40) cc_final: 0.7955 (mm110) REVERT: c 536 THR cc_start: 0.9269 (p) cc_final: 0.8980 (t) REVERT: c 601 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8300 (mtpp) REVERT: c 621 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8288 (pp20) REVERT: g 656 ASN cc_start: 0.8887 (m-40) cc_final: 0.8603 (m-40) outliers start: 50 outliers final: 30 residues processed: 154 average time/residue: 0.6195 time to fit residues: 106.4836 Evaluate side-chains 137 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 134 VAL Chi-restraints excluded: chain b residue 242 VAL Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 452 LEU Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain c residue 601 LYS Chi-restraints excluded: chain c residue 620 ASP Chi-restraints excluded: chain c residue 621 GLU Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain c residue 654 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 119 CYS Chi-restraints excluded: chain d residue 195 ASN Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain e residue 546 SER Chi-restraints excluded: chain e residue 599 SER Chi-restraints excluded: chain e residue 604 CYS Chi-restraints excluded: chain e residue 612 SER Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain e residue 655 LYS Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 51 THR Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 488 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 61 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 60 optimal weight: 0.0070 chunk 125 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 164 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 overall best weight: 1.1204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.077500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.059998 restraints weight = 50307.350| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.73 r_work: 0.3043 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17738 Z= 0.137 Angle : 0.688 17.298 24295 Z= 0.310 Chirality : 0.045 0.275 3019 Planarity : 0.003 0.037 2856 Dihedral : 8.712 104.565 4729 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.61 % Allowed : 14.42 % Favored : 82.98 % 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: -0.18 (0.19), residues: 1910 helix: 0.57 (0.28), residues: 387 sheet: 0.05 (0.23), residues: 465 loop : -0.39 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG c 644 TYR 0.015 0.001 TYR c 638 PHE 0.011 0.001 PHE b 383 TRP 0.012 0.001 TRP b 96 HIS 0.003 0.001 HIS f 130 Details of bonding type rmsd covalent geometry : bond 0.00322 (17574) covalent geometry : angle 0.61005 (23841) SS BOND : bond 0.00287 ( 38) SS BOND : angle 1.53511 ( 76) hydrogen bonds : bond 0.03600 ( 554) hydrogen bonds : angle 5.20315 ( 1557) link_ALPHA1-3 : bond 0.01082 ( 5) link_ALPHA1-3 : angle 1.93592 ( 15) link_ALPHA1-6 : bond 0.00889 ( 4) link_ALPHA1-6 : angle 2.07767 ( 12) link_BETA1-4 : bond 0.00565 ( 48) link_BETA1-4 : angle 2.61806 ( 144) link_NAG-ASN : bond 0.00286 ( 69) link_NAG-ASN : angle 2.54334 ( 207) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 113 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 16 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8075 (pm20) REVERT: H 40 MET cc_start: 0.8889 (mmm) cc_final: 0.8675 (mpt) REVERT: L 45 LYS cc_start: 0.8984 (ttmm) cc_final: 0.8647 (tttp) REVERT: L 79 GLN cc_start: 0.8404 (mm-40) cc_final: 0.7950 (mm110) REVERT: c 520 ARG cc_start: 0.7940 (mmm-85) cc_final: 0.7694 (mtt180) REVERT: c 536 THR cc_start: 0.9256 (p) cc_final: 0.8955 (t) REVERT: c 601 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8324 (mtpp) REVERT: g 656 ASN cc_start: 0.8890 (m-40) cc_final: 0.8595 (m-40) outliers start: 45 outliers final: 28 residues processed: 149 average time/residue: 0.5792 time to fit residues: 97.3033 Evaluate side-chains 134 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 134 VAL Chi-restraints excluded: chain b residue 242 VAL Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 452 LEU Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain c residue 601 LYS Chi-restraints excluded: chain c residue 620 ASP Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain c residue 654 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 119 CYS Chi-restraints excluded: chain d residue 195 ASN Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain e residue 546 SER Chi-restraints excluded: chain e residue 599 SER Chi-restraints excluded: chain e residue 604 CYS Chi-restraints excluded: chain e residue 612 SER Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain e residue 655 LYS Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 51 THR Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 488 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 106 optimal weight: 7.9990 chunk 96 optimal weight: 0.1980 chunk 190 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 60 optimal weight: 0.0270 chunk 1 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 172 optimal weight: 0.1980 chunk 39 optimal weight: 3.9990 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.078896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.061363 restraints weight = 50447.786| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.76 r_work: 0.3106 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17738 Z= 0.107 Angle : 0.664 17.184 24295 Z= 0.300 Chirality : 0.045 0.274 3019 Planarity : 0.003 0.038 2856 Dihedral : 8.391 102.568 4729 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.14 % Allowed : 15.29 % Favored : 82.57 % 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: -0.05 (0.19), residues: 1910 helix: 0.93 (0.29), residues: 369 sheet: -0.05 (0.22), residues: 498 loop : -0.30 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 644 TYR 0.015 0.001 TYR c 638 PHE 0.007 0.001 PHE b 383 TRP 0.014 0.001 TRP g 631 HIS 0.003 0.001 HIS f 130 Details of bonding type rmsd covalent geometry : bond 0.00233 (17574) covalent geometry : angle 0.59125 (23841) SS BOND : bond 0.00256 ( 38) SS BOND : angle 1.19595 ( 76) hydrogen bonds : bond 0.03351 ( 554) hydrogen bonds : angle 5.11852 ( 1557) link_ALPHA1-3 : bond 0.01046 ( 5) link_ALPHA1-3 : angle 1.80231 ( 15) link_ALPHA1-6 : bond 0.01106 ( 4) link_ALPHA1-6 : angle 2.07780 ( 12) link_BETA1-4 : bond 0.00567 ( 48) link_BETA1-4 : angle 2.53495 ( 144) link_NAG-ASN : bond 0.00294 ( 69) link_NAG-ASN : angle 2.45731 ( 207) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8983 (ttmm) cc_final: 0.8605 (mmmm) REVERT: L 45 LYS cc_start: 0.9056 (ttmm) cc_final: 0.8748 (tttp) REVERT: L 79 GLN cc_start: 0.8406 (mm-40) cc_final: 0.7951 (mm110) REVERT: c 520 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.7660 (mtt180) REVERT: c 536 THR cc_start: 0.9257 (p) cc_final: 0.8950 (t) REVERT: c 601 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8340 (mtpp) REVERT: c 633 LYS cc_start: 0.8536 (ptpp) cc_final: 0.7909 (mptt) REVERT: g 656 ASN cc_start: 0.8905 (m-40) cc_final: 0.8612 (m-40) outliers start: 37 outliers final: 27 residues processed: 150 average time/residue: 0.6110 time to fit residues: 102.6210 Evaluate side-chains 139 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 242 VAL Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 452 LEU Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain c residue 601 LYS Chi-restraints excluded: chain c residue 620 ASP Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain c residue 654 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 119 CYS Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 195 ASN Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain e residue 546 SER Chi-restraints excluded: chain e residue 599 SER Chi-restraints excluded: chain e residue 604 CYS Chi-restraints excluded: chain e residue 612 SER Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain e residue 655 LYS Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 181 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 43 optimal weight: 0.0050 chunk 177 optimal weight: 0.6980 chunk 189 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 425 ASN d 195 ASN f 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.077855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.060226 restraints weight = 50664.573| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.75 r_work: 0.3073 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17738 Z= 0.162 Angle : 0.692 17.153 24295 Z= 0.312 Chirality : 0.046 0.280 3019 Planarity : 0.003 0.039 2856 Dihedral : 8.316 101.888 4729 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.55 % Allowed : 15.11 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.06 (0.19), residues: 1910 helix: 0.92 (0.29), residues: 369 sheet: -0.01 (0.22), residues: 513 loop : -0.32 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 644 TYR 0.017 0.001 TYR c 638 PHE 0.011 0.001 PHE b 383 TRP 0.012 0.001 TRP H 83 HIS 0.003 0.001 HIS f 130 Details of bonding type rmsd covalent geometry : bond 0.00388 (17574) covalent geometry : angle 0.62069 (23841) SS BOND : bond 0.00291 ( 38) SS BOND : angle 1.22744 ( 76) hydrogen bonds : bond 0.03519 ( 554) hydrogen bonds : angle 5.11350 ( 1557) link_ALPHA1-3 : bond 0.01015 ( 5) link_ALPHA1-3 : angle 1.91772 ( 15) link_ALPHA1-6 : bond 0.00997 ( 4) link_ALPHA1-6 : angle 2.10306 ( 12) link_BETA1-4 : bond 0.00563 ( 48) link_BETA1-4 : angle 2.54314 ( 144) link_NAG-ASN : bond 0.00295 ( 69) link_NAG-ASN : angle 2.50178 ( 207) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 109 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.9009 (ttmm) cc_final: 0.8632 (mmmm) REVERT: H 46 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8819 (mt-10) REVERT: L 45 LYS cc_start: 0.9052 (ttmm) cc_final: 0.8742 (tttp) REVERT: L 79 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7953 (mm110) REVERT: c 520 ARG cc_start: 0.7963 (mmm-85) cc_final: 0.7707 (mtt180) REVERT: c 536 THR cc_start: 0.9263 (p) cc_final: 0.8952 (t) REVERT: c 601 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8344 (mtpp) REVERT: g 656 ASN cc_start: 0.8889 (m-40) cc_final: 0.8591 (m-40) REVERT: g 659 GLU cc_start: 0.7232 (tt0) cc_final: 0.6915 (tt0) outliers start: 44 outliers final: 30 residues processed: 144 average time/residue: 0.5851 time to fit residues: 94.6729 Evaluate side-chains 139 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 134 VAL Chi-restraints excluded: chain b residue 242 VAL Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 452 LEU Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain c residue 601 LYS Chi-restraints excluded: chain c residue 620 ASP Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain c residue 654 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 119 CYS Chi-restraints excluded: chain d residue 195 ASN Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain e residue 546 SER Chi-restraints excluded: chain e residue 599 SER Chi-restraints excluded: chain e residue 604 CYS Chi-restraints excluded: chain e residue 612 SER Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain e residue 655 LYS Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 80 ASN Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 488 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 141 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 73 optimal weight: 0.0770 chunk 66 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 overall best weight: 1.2544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.079041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.060905 restraints weight = 50927.102| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.80 r_work: 0.3072 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17738 Z= 0.146 Angle : 0.691 17.102 24295 Z= 0.311 Chirality : 0.045 0.277 3019 Planarity : 0.003 0.037 2856 Dihedral : 8.235 101.351 4729 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.61 % Allowed : 15.17 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1910 helix: 0.93 (0.30), residues: 369 sheet: 0.00 (0.22), residues: 498 loop : -0.36 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 644 TYR 0.018 0.001 TYR L 49 PHE 0.011 0.001 PHE b 383 TRP 0.015 0.001 TRP g 631 HIS 0.003 0.001 HIS f 130 Details of bonding type rmsd covalent geometry : bond 0.00348 (17574) covalent geometry : angle 0.62136 (23841) SS BOND : bond 0.00282 ( 38) SS BOND : angle 1.16434 ( 76) hydrogen bonds : bond 0.03506 ( 554) hydrogen bonds : angle 5.09573 ( 1557) link_ALPHA1-3 : bond 0.01024 ( 5) link_ALPHA1-3 : angle 1.87543 ( 15) link_ALPHA1-6 : bond 0.01120 ( 4) link_ALPHA1-6 : angle 2.10072 ( 12) link_BETA1-4 : bond 0.00548 ( 48) link_BETA1-4 : angle 2.51375 ( 144) link_NAG-ASN : bond 0.00282 ( 69) link_NAG-ASN : angle 2.48604 ( 207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 112 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.9010 (ttmm) cc_final: 0.8635 (mmmm) REVERT: H 46 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8839 (mt-10) REVERT: H 103 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8882 (tt) REVERT: L 45 LYS cc_start: 0.9050 (ttmm) cc_final: 0.8731 (tttp) REVERT: L 79 GLN cc_start: 0.8382 (mm-40) cc_final: 0.7933 (mm110) REVERT: c 520 ARG cc_start: 0.7985 (mmm-85) cc_final: 0.7724 (mtt180) REVERT: c 536 THR cc_start: 0.9267 (p) cc_final: 0.8946 (t) REVERT: c 601 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8332 (mtpp) REVERT: c 633 LYS cc_start: 0.8465 (ptpp) cc_final: 0.7990 (mptp) REVERT: g 656 ASN cc_start: 0.8886 (m-40) cc_final: 0.8584 (m-40) REVERT: g 659 GLU cc_start: 0.7189 (tt0) cc_final: 0.6873 (tt0) outliers start: 45 outliers final: 32 residues processed: 146 average time/residue: 0.5936 time to fit residues: 97.5303 Evaluate side-chains 142 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 134 VAL Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain b residue 242 VAL Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 452 LEU Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain c residue 601 LYS Chi-restraints excluded: chain c residue 620 ASP Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain c residue 654 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 119 CYS Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 378 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain e residue 546 SER Chi-restraints excluded: chain e residue 599 SER Chi-restraints excluded: chain e residue 604 CYS Chi-restraints excluded: chain e residue 612 SER Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain e residue 655 LYS Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 488 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.078973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.060784 restraints weight = 50742.452| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.80 r_work: 0.3062 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17738 Z= 0.166 Angle : 0.700 17.089 24295 Z= 0.317 Chirality : 0.046 0.278 3019 Planarity : 0.003 0.039 2856 Dihedral : 8.192 100.738 4729 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.20 % Allowed : 15.63 % Favored : 82.17 % 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: -0.07 (0.19), residues: 1910 helix: 0.91 (0.30), residues: 369 sheet: 0.01 (0.22), residues: 513 loop : -0.36 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 644 TYR 0.020 0.001 TYR c 638 PHE 0.012 0.001 PHE b 383 TRP 0.017 0.001 TRP c 631 HIS 0.003 0.001 HIS f 130 Details of bonding type rmsd covalent geometry : bond 0.00401 (17574) covalent geometry : angle 0.63144 (23841) SS BOND : bond 0.00304 ( 38) SS BOND : angle 1.20496 ( 76) hydrogen bonds : bond 0.03589 ( 554) hydrogen bonds : angle 5.10808 ( 1557) link_ALPHA1-3 : bond 0.00995 ( 5) link_ALPHA1-3 : angle 1.89066 ( 15) link_ALPHA1-6 : bond 0.01125 ( 4) link_ALPHA1-6 : angle 2.14830 ( 12) link_BETA1-4 : bond 0.00545 ( 48) link_BETA1-4 : angle 2.49930 ( 144) link_NAG-ASN : bond 0.00293 ( 69) link_NAG-ASN : angle 2.49775 ( 207) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.9013 (ttmm) cc_final: 0.8638 (mmmm) REVERT: H 46 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8823 (mt-10) REVERT: H 87 LYS cc_start: 0.8382 (mtmm) cc_final: 0.8090 (mptp) REVERT: H 103 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8882 (tt) REVERT: L 45 LYS cc_start: 0.9045 (ttmm) cc_final: 0.8723 (tttp) REVERT: L 79 GLN cc_start: 0.8382 (mm-40) cc_final: 0.7929 (mm110) REVERT: c 520 ARG cc_start: 0.7981 (mmm-85) cc_final: 0.7713 (mtt180) REVERT: c 536 THR cc_start: 0.9262 (p) cc_final: 0.8921 (t) REVERT: c 601 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8330 (mtpp) REVERT: g 656 ASN cc_start: 0.8885 (m-40) cc_final: 0.8582 (m-40) REVERT: g 659 GLU cc_start: 0.7178 (tt0) cc_final: 0.6866 (tt0) outliers start: 38 outliers final: 32 residues processed: 145 average time/residue: 0.5999 time to fit residues: 97.8241 Evaluate side-chains 143 residues out of total 1727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 134 VAL Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain b residue 242 VAL Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 452 LEU Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain c residue 601 LYS Chi-restraints excluded: chain c residue 648 GLU Chi-restraints excluded: chain c residue 654 GLU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 119 CYS Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 323 ILE Chi-restraints excluded: chain d residue 378 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain e residue 546 SER Chi-restraints excluded: chain e residue 599 SER Chi-restraints excluded: chain e residue 604 CYS Chi-restraints excluded: chain e residue 612 SER Chi-restraints excluded: chain e residue 638 TYR Chi-restraints excluded: chain e residue 655 LYS Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 488 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 38 optimal weight: 2.9990 chunk 131 optimal weight: 0.0060 chunk 149 optimal weight: 0.6980 chunk 182 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.079237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.061075 restraints weight = 50906.241| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.80 r_work: 0.3063 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17738 Z= 0.153 Angle : 0.702 17.079 24295 Z= 0.319 Chirality : 0.045 0.275 3019 Planarity : 0.003 0.041 2856 Dihedral : 8.071 99.778 4729 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.14 % Allowed : 15.92 % Favored : 81.93 % 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: -0.07 (0.19), residues: 1910 helix: 0.96 (0.30), residues: 369 sheet: 0.02 (0.22), residues: 498 loop : -0.38 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 644 TYR 0.019 0.001 TYR c 638 PHE 0.011 0.001 PHE b 383 TRP 0.017 0.001 TRP c 631 HIS 0.003 0.001 HIS f 130 Details of bonding type rmsd covalent geometry : bond 0.00368 (17574) covalent geometry : angle 0.63455 (23841) SS BOND : bond 0.00279 ( 38) SS BOND : angle 1.16842 ( 76) hydrogen bonds : bond 0.03556 ( 554) hydrogen bonds : angle 5.08033 ( 1557) link_ALPHA1-3 : bond 0.00992 ( 5) link_ALPHA1-3 : angle 1.85483 ( 15) link_ALPHA1-6 : bond 0.01273 ( 4) link_ALPHA1-6 : angle 2.22245 ( 12) link_BETA1-4 : bond 0.00546 ( 48) link_BETA1-4 : angle 2.46147 ( 144) link_NAG-ASN : bond 0.00282 ( 69) link_NAG-ASN : angle 2.47915 ( 207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4638.29 seconds wall clock time: 80 minutes 20.94 seconds (4820.94 seconds total)