Starting phenix.real_space_refine on Sun Sep 13 03:02:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6myy_9294/09_2026/6myy_9294.cif Found real_map, /net/cci-nas-00/data/ceres_data/6myy_9294/09_2026/6myy_9294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6myy_9294/09_2026/6myy_9294.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6myy_9294/09_2026/6myy_9294.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6myy_9294/09_2026/6myy_9294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6myy_9294/09_2026/6myy_9294.map" model { file = "/net/cci-nas-00/data/ceres_data/6myy_9294/09_2026/6myy_9294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6myy_9294/09_2026/6myy_9294.cif" } resolution = 3.8 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= 0.007 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 129 5.16 5 C 12564 2.51 5 N 3243 2.21 5 O 4203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20139 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4338 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 23, 'TRANS': 526} Chain breaks: 5 Chain: "L" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 767 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4338 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 23, 'TRANS': 526} Chain breaks: 5 Chain: "C" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 767 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain: "D" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4338 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 23, 'TRANS': 526} Chain breaks: 5 Chain: "F" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 767 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain: "G" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 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 chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "N" 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 chiralities: 3 Chain: "O" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 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 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 chiralities: 2 Chain: "T" 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 chiralities: 5 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 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 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 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 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 chiralities: 2 Chain: "Z" 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 chiralities: 5 Chain: "a" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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 chiralities: 3 Chain: "c" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "e" 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 chiralities: 3 Chain: "f" 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 chiralities: 4 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 chiralities: 2 Chain: "h" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "n" 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 chiralities: 5 Chain: "o" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "t" 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 chiralities: 4 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 chiralities: 2 Chain: "v" 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 chiralities: 5 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 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 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 chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.67, per 1000 atoms: 0.23 Number of scatterers: 20139 At special positions: 0 Unit cell: (149.6, 140.08, 125.12, 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 129 16.00 O 4203 8.00 N 3243 7.00 C 12564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.13 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.05 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS H 60 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 605 " distance=2.20 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.17 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.13 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.02 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 459 " - pdb=" SG CYS D 60 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 605 " distance=2.20 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.17 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.13 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.05 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 459 " - pdb=" SG CYS G 60 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS E 605 " distance=2.20 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.17 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " 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 ALPHA1-2 " MAN O 4 " - " MAN O 5 " " MAN T 4 " - " MAN T 5 " " MAN c 4 " - " MAN c 5 " " MAN h 4 " - " MAN h 5 " " MAN q 4 " - " MAN q 5 " " MAN v 4 " - " MAN v 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 6 " " MAN M 4 " - " MAN M 5 " " BMA O 3 " - " MAN O 4 " " MAN O 6 " - " MAN O 7 " " BMA R 3 " - " MAN R 4 " " BMA T 3 " - " MAN T 4 " " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 6 " " MAN a 4 " - " MAN a 5 " " BMA c 3 " - " MAN c 4 " " MAN c 6 " - " MAN c 7 " " BMA f 3 " - " MAN f 4 " " BMA h 3 " - " MAN h 4 " " BMA n 3 " - " MAN n 4 " " BMA o 3 " - " MAN o 6 " " MAN o 4 " - " MAN o 5 " " BMA q 3 " - " MAN q 4 " " MAN q 6 " - " MAN q 7 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 6 " " BMA Z 3 " - " MAN Z 5 " " BMA a 3 " - " MAN a 4 " " BMA c 3 " - " MAN c 6 " " BMA n 3 " - " MAN n 5 " " BMA o 3 " - " MAN o 4 " " BMA q 3 " - " MAN q 6 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " 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 d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG A 738 " - " ASN A 357 " " NAG A 744 " - " ASN A 411 " " NAG A 747 " - " ASN A 611 " " NAG A 748 " - " ASN A 637 " " NAG B 738 " - " ASN B 357 " " NAG B 744 " - " ASN B 411 " " NAG B 747 " - " ASN B 611 " " NAG B 748 " - " ASN B 637 " " NAG E 738 " - " ASN E 357 " " NAG E 744 " - " ASN E 411 " " NAG E 747 " - " ASN E 611 " " NAG E 748 " - " ASN E 637 " " NAG I 1 " - " ASN A 88 " " NAG J 1 " - " ASN A 130 " " NAG K 1 " - " ASN A 156 " " NAG M 1 " - " ASN A 197 " " NAG N 1 " - " ASN A 241 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN A 289 " " NAG Q 1 " - " ASN A 301 " " NAG R 1 " - " ASN A 332 " " NAG S 1 " - " ASN A 337 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 442 " " NAG V 1 " - " ASN A 230 " " NAG W 1 " - " ASN A 392 " " NAG X 1 " - " ASN B 88 " " NAG Y 1 " - " ASN B 130 " " NAG Z 1 " - " ASN B 156 " " NAG a 1 " - " ASN B 197 " " NAG b 1 " - " ASN B 241 " " NAG c 1 " - " ASN B 262 " " NAG d 1 " - " ASN B 289 " " NAG e 1 " - " ASN B 301 " " NAG f 1 " - " ASN B 332 " " NAG g 1 " - " ASN B 337 " " NAG h 1 " - " ASN B 386 " " NAG i 1 " - " ASN B 442 " " NAG j 1 " - " ASN B 230 " " NAG k 1 " - " ASN B 392 " " NAG l 1 " - " ASN E 88 " " NAG m 1 " - " ASN E 130 " " NAG n 1 " - " ASN E 156 " " NAG o 1 " - " ASN E 197 " " NAG p 1 " - " ASN E 241 " " NAG q 1 " - " ASN E 262 " " NAG r 1 " - " ASN E 289 " " NAG s 1 " - " ASN E 301 " " NAG t 1 " - " ASN E 332 " " NAG u 1 " - " ASN E 337 " " NAG v 1 " - " ASN E 386 " " NAG w 1 " - " ASN E 442 " " NAG x 1 " - " ASN E 230 " " NAG y 1 " - " ASN E 392 " Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 802.1 milliseconds 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4290 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 45 sheets defined 22.0% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.229A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.769A pdb=" N HIS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'A' and resid 523 through 528 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 542 Processing helix chain 'A' and resid 571 through 596 Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.612A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 662 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.114A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'B' and resid 98 through 116 removed outlier: 4.228A pdb=" N ASP B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 334 through 353 removed outlier: 3.769A pdb=" N HIS B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 475 through 481 Processing helix chain 'B' and resid 482 through 484 No H-bonds generated for 'chain 'B' and resid 482 through 484' Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 571 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.612A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'D' and resid 28 through 32 removed outlier: 4.114A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.229A pdb=" N ASP E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 334 through 353 removed outlier: 3.769A pdb=" N HIS E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 481 Processing helix chain 'E' and resid 482 through 484 No H-bonds generated for 'chain 'E' and resid 482 through 484' Processing helix chain 'E' and resid 523 through 528 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 542 Processing helix chain 'E' and resid 571 through 596 Processing helix chain 'E' and resid 618 through 625 Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.612A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 662 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 28 through 32 removed outlier: 4.114A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.266A pdb=" N VAL A 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL A 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N THR A 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N TYR A 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N CYS A 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.831A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.240A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.503A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY A 451 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 10.778A pdb=" N LYS A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.955A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N LEU A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.905A pdb=" N VAL A 286 " --> pdb=" O LEU A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 357 through 361 Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 10.905A pdb=" N VAL A 286 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N LEU A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.955A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.778A pdb=" N LYS A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY A 451 " --> pdb=" O LYS A 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 414 through 420 removed outlier: 3.576A pdb=" N PHE A 383 " --> pdb=" O PHE A 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 302 through 312 removed outlier: 6.390A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.777A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.460A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.460A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.566A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AB7, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.266A pdb=" N VAL B 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL B 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N THR B 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N TYR B 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N CYS B 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.832A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AC3, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.240A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.502A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY B 451 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 10.779A pdb=" N LYS B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N LEU B 453 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 11.955A pdb=" N LEU B 288 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N LEU B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 10.906A pdb=" N VAL B 286 " --> pdb=" O LEU B 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 284 through 298 current: chain 'B' and resid 357 through 361 Processing sheet with id=AC5, first strand: chain 'B' and resid 271 through 273 removed outlier: 10.906A pdb=" N VAL B 286 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N LEU B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.955A pdb=" N LEU B 288 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N LEU B 453 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 10.779A pdb=" N LYS B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY B 451 " --> pdb=" O LYS B 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 443 through 456 current: chain 'B' and resid 414 through 420 removed outlier: 3.576A pdb=" N PHE B 383 " --> pdb=" O PHE B 376 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 302 through 312 removed outlier: 6.390A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.777A pdb=" N SER C 7 " --> pdb=" O SER C 22 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.459A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.459A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.566A pdb=" N MET D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TRP D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AD4, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.266A pdb=" N VAL E 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL E 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N THR E 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N TYR E 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N CYS E 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.832A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD9, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.240A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.502A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY E 451 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 10.779A pdb=" N LYS E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.955A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N LEU E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.905A pdb=" N VAL E 286 " --> pdb=" O LEU E 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 298 current: chain 'E' and resid 357 through 361 Processing sheet with id=AE2, first strand: chain 'E' and resid 271 through 273 removed outlier: 10.905A pdb=" N VAL E 286 " --> pdb=" O LEU E 455 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N LEU E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.955A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.779A pdb=" N LYS E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY E 451 " --> pdb=" O LYS E 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 443 through 456 current: chain 'E' and resid 414 through 420 removed outlier: 3.576A pdb=" N PHE E 383 " --> pdb=" O PHE E 376 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 302 through 312 removed outlier: 6.390A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 5 through 7 removed outlier: 3.777A pdb=" N SER F 7 " --> pdb=" O SER F 22 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.460A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.460A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.565A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 10 through 11 780 hydrogen bonds defined for protein. 1953 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: 4.02 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4680 1.33 - 1.45: 4605 1.45 - 1.57: 11013 1.57 - 1.70: 60 1.70 - 1.82: 168 Bond restraints: 20526 Sorted by residual: bond pdb=" C5 BMA c 3 " pdb=" C6 BMA c 3 " ideal model delta sigma weight residual 1.526 1.610 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C5 BMA O 3 " pdb=" C6 BMA O 3 " ideal model delta sigma weight residual 1.526 1.610 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C5 BMA q 3 " pdb=" C6 BMA q 3 " ideal model delta sigma weight residual 1.526 1.609 -0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C5 BMA M 3 " pdb=" C6 BMA M 3 " ideal model delta sigma weight residual 1.526 1.607 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C5 BMA o 3 " pdb=" C6 BMA o 3 " ideal model delta sigma weight residual 1.526 1.607 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 20521 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 24311 1.71 - 3.43: 2717 3.43 - 5.14: 441 5.14 - 6.85: 302 6.85 - 8.57: 96 Bond angle restraints: 27867 Sorted by residual: angle pdb=" C ALA B 436 " pdb=" N PRO B 437 " pdb=" CA PRO B 437 " ideal model delta sigma weight residual 119.66 126.41 -6.75 7.20e-01 1.93e+00 8.78e+01 angle pdb=" C ALA E 436 " pdb=" N PRO E 437 " pdb=" CA PRO E 437 " ideal model delta sigma weight residual 119.66 126.40 -6.74 7.20e-01 1.93e+00 8.77e+01 angle pdb=" C ALA A 436 " pdb=" N PRO A 437 " pdb=" CA PRO A 437 " ideal model delta sigma weight residual 119.66 126.39 -6.73 7.20e-01 1.93e+00 8.74e+01 angle pdb=" C PHE E 353 " pdb=" N PRO E 354 " pdb=" CA PRO E 354 " ideal model delta sigma weight residual 119.56 128.13 -8.57 1.01e+00 9.80e-01 7.20e+01 angle pdb=" C PHE A 353 " pdb=" N PRO A 354 " pdb=" CA PRO A 354 " ideal model delta sigma weight residual 119.56 128.12 -8.56 1.01e+00 9.80e-01 7.18e+01 ... (remaining 27862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 10628 17.23 - 34.46: 352 34.46 - 51.69: 117 51.69 - 68.92: 54 68.92 - 86.15: 12 Dihedral angle restraints: 11163 sinusoidal: 4500 harmonic: 6663 Sorted by residual: dihedral pdb=" CA PHE E 353 " pdb=" C PHE E 353 " pdb=" N PRO E 354 " pdb=" CA PRO E 354 " ideal model delta harmonic sigma weight residual -180.00 -154.39 -25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA PHE B 353 " pdb=" C PHE B 353 " pdb=" N PRO B 354 " pdb=" CA PRO B 354 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA PHE A 353 " pdb=" C PHE A 353 " pdb=" N PRO A 354 " pdb=" CA PRO A 354 " ideal model delta harmonic sigma weight residual -180.00 -154.48 -25.52 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 11160 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 3300 0.130 - 0.261: 238 0.261 - 0.391: 20 0.391 - 0.521: 0 0.521 - 0.651: 24 Chirality restraints: 3582 Sorted by residual: chirality pdb=" C1 BMA c 3 " pdb=" O4 NAG c 2 " pdb=" C2 BMA c 3 " pdb=" O5 BMA c 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.90e+02 chirality pdb=" C1 BMA q 3 " pdb=" O4 NAG q 2 " pdb=" C2 BMA q 3 " pdb=" O5 BMA q 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.89e+02 chirality pdb=" C1 BMA O 3 " pdb=" O4 NAG O 2 " pdb=" C2 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.89e+02 ... (remaining 3579 not shown) Planarity restraints: 3366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 301 " -0.026 2.00e-02 2.50e+03 2.78e-02 9.67e+00 pdb=" CG ASN E 301 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN E 301 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN E 301 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG s 1 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 301 " -0.026 2.00e-02 2.50e+03 2.78e-02 9.66e+00 pdb=" CG ASN A 301 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN A 301 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 301 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 301 " -0.026 2.00e-02 2.50e+03 2.78e-02 9.65e+00 pdb=" CG ASN B 301 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN B 301 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 301 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG e 1 " -0.034 2.00e-02 2.50e+03 ... (remaining 3363 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6348 2.82 - 3.34: 17753 3.34 - 3.86: 33313 3.86 - 4.38: 38387 4.38 - 4.90: 62472 Nonbonded interactions: 158273 Sorted by model distance: nonbonded pdb=" OD1 ASP B 107 " pdb=" NZ LYS B 574 " model vdw 2.302 3.120 nonbonded pdb=" OD1 ASP E 107 " pdb=" NZ LYS E 574 " model vdw 2.303 3.120 nonbonded pdb=" OD1 ASP A 107 " pdb=" NZ LYS A 574 " model vdw 2.303 3.120 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.328 3.040 nonbonded pdb=" OG1 THR E 37 " pdb=" OG1 THR E 499 " model vdw 2.329 3.040 ... (remaining 158268 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'u' selection = chain 'w' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'K' selection = chain 'T' selection = chain 'Z' selection = chain 'h' selection = chain 'n' selection = chain 'v' } ncs_group { reference = (chain 'M' and (resid 1 or resid 4 through 6)) selection = (chain 'O' and (resid 2 or resid 5 through 7)) selection = (chain 'a' and (resid 1 or resid 4 through 6)) selection = (chain 'c' and (resid 2 or resid 5 through 7)) selection = (chain 'o' and (resid 1 or resid 4 through 6)) selection = (chain 'q' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'p' selection = chain 'r' selection = chain 's' } ncs_group { reference = chain 'R' selection = chain 'f' selection = chain 't' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.090 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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 : 0.016 0.167 20727 Z= 0.834 Angle : 1.394 13.399 28425 Z= 0.805 Chirality : 0.089 0.651 3582 Planarity : 0.003 0.013 3312 Dihedral : 11.032 86.149 6738 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.32 % Favored : 96.54 % Rotamer: Outliers : 0.30 % Allowed : 1.34 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.23 (0.17), residues: 2256 helix: -0.17 (0.25), residues: 411 sheet: 0.08 (0.19), residues: 717 loop : -0.16 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 298 TYR 0.016 0.002 TYR B 484 PHE 0.014 0.002 PHE E 383 TRP 0.017 0.002 TRP D 47 HIS 0.002 0.000 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.01540 / 0.82 (20526) covalent geometry : angle 1.36600 / 0.80 (27867) SS BOND : bond 0.06274 / 3.75 ( 45) SS BOND : angle 3.92436 / 2.67 ( 90) hydrogen bonds : bond 0.19042 / 12.55 ( 705) hydrogen bonds : angle 8.02491 / 5.74 ( 1953) link_ALPHA1-2 : bond 0.02810 / 1.48 ( 6) link_ALPHA1-2 : angle 1.02245 / 0.58 ( 18) link_ALPHA1-3 : bond 0.03279 / 2.01 ( 21) link_ALPHA1-3 : angle 1.25054 / 0.88 ( 63) link_ALPHA1-6 : bond 0.03163 / 1.74 ( 9) link_ALPHA1-6 : angle 2.35843 / 1.51 ( 27) link_BETA1-4 : bond 0.03171 / 2.00 ( 66) link_BETA1-4 : angle 1.80751 / 1.23 ( 198) link_NAG-ASN : bond 0.02289 / 1.50 ( 54) link_NAG-ASN : angle 2.41139 / 1.64 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 301 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ASN cc_start: 0.8159 (t0) cc_final: 0.7832 (t0) REVERT: A 464 ASN cc_start: 0.7894 (m-40) cc_final: 0.7379 (t0) REVERT: H 48 MET cc_start: 0.7465 (mmm) cc_final: 0.7075 (mmt) REVERT: B 125 LEU cc_start: 0.9103 (mm) cc_final: 0.8880 (mt) REVERT: B 377 ASN cc_start: 0.8297 (t0) cc_final: 0.7694 (t0) REVERT: B 464 ASN cc_start: 0.7696 (m-40) cc_final: 0.7388 (t0) REVERT: C 32 TYR cc_start: 0.7653 (m-80) cc_final: 0.6764 (m-10) REVERT: D 51 ILE cc_start: 0.9263 (tt) cc_final: 0.9060 (tt) REVERT: D 85 ASP cc_start: 0.8313 (p0) cc_final: 0.8072 (p0) REVERT: E 69 TRP cc_start: 0.8257 (m-90) cc_final: 0.7334 (m-10) REVERT: E 377 ASN cc_start: 0.8376 (t0) cc_final: 0.7932 (t0) REVERT: E 464 ASN cc_start: 0.7592 (m-40) cc_final: 0.7087 (t0) REVERT: G 85 ASP cc_start: 0.8538 (p0) cc_final: 0.8266 (p0) outliers start: 6 outliers final: 0 residues processed: 307 average time/residue: 0.1354 time to fit residues: 65.9914 Evaluate side-chains 112 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 HIS L 37 GLN B 216 HIS B 543 ASN C 37 GLN E 216 HIS E 374 HIS F 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.070304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.058552 restraints weight = 87591.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.060198 restraints weight = 47074.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.061300 restraints weight = 31883.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.062019 restraints weight = 25000.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.062488 restraints weight = 21387.838| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20727 Z= 0.149 Angle : 0.716 14.486 28425 Z= 0.335 Chirality : 0.045 0.426 3582 Planarity : 0.004 0.036 3312 Dihedral : 4.048 22.219 2484 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.95 % Favored : 97.92 % Rotamer: Outliers : 1.04 % Allowed : 6.57 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.18), residues: 2256 helix: 1.72 (0.27), residues: 408 sheet: 0.38 (0.19), residues: 735 loop : 0.32 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 83 TYR 0.020 0.001 TYR D 90 PHE 0.016 0.002 PHE B 382 TRP 0.013 0.001 TRP A 69 HIS 0.003 0.001 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (20526) covalent geometry : angle 0.67949 / 0.33 (27867) SS BOND : bond 0.00232 / 0.16 ( 45) SS BOND : angle 0.96740 / 0.64 ( 90) hydrogen bonds : bond 0.05586 / 3.70 ( 705) hydrogen bonds : angle 6.07479 / 4.30 ( 1953) link_ALPHA1-2 : bond 0.00765 / 0.42 ( 6) link_ALPHA1-2 : angle 1.46546 / 0.91 ( 18) link_ALPHA1-3 : bond 0.00679 / 0.42 ( 21) link_ALPHA1-3 : angle 1.39589 / 0.98 ( 63) link_ALPHA1-6 : bond 0.00828 / 0.45 ( 9) link_ALPHA1-6 : angle 1.38224 / 0.88 ( 27) link_BETA1-4 : bond 0.00493 / 0.33 ( 66) link_BETA1-4 : angle 1.88495 / 1.25 ( 198) link_NAG-ASN : bond 0.00281 / 0.21 ( 54) link_NAG-ASN : angle 2.06331 / 1.44 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ASN cc_start: 0.8340 (t0) cc_final: 0.8033 (t0) REVERT: A 426 MET cc_start: 0.8312 (mmm) cc_final: 0.7680 (tpp) REVERT: A 464 ASN cc_start: 0.7844 (m-40) cc_final: 0.7303 (t0) REVERT: B 69 TRP cc_start: 0.8461 (m-10) cc_final: 0.7538 (m-10) REVERT: B 86 LEU cc_start: 0.8995 (mp) cc_final: 0.8767 (mp) REVERT: B 377 ASN cc_start: 0.8332 (t0) cc_final: 0.7987 (t0) REVERT: B 464 ASN cc_start: 0.7247 (m-40) cc_final: 0.7027 (t0) REVERT: E 69 TRP cc_start: 0.8437 (m-90) cc_final: 0.7382 (m-10) REVERT: E 100 MET cc_start: 0.8602 (mtp) cc_final: 0.8381 (mtp) REVERT: E 377 ASN cc_start: 0.8375 (t0) cc_final: 0.8018 (t0) REVERT: E 464 ASN cc_start: 0.7207 (m-40) cc_final: 0.6796 (t0) REVERT: F 87 TYR cc_start: 0.8055 (m-80) cc_final: 0.7823 (m-80) REVERT: G 69 MET cc_start: 0.8405 (mtm) cc_final: 0.8184 (mtt) REVERT: G 85 ASP cc_start: 0.9011 (p0) cc_final: 0.8752 (p0) outliers start: 21 outliers final: 12 residues processed: 168 average time/residue: 0.1320 time to fit residues: 36.4320 Evaluate side-chains 125 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 42 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 ASN A 355 HIS A 422 GLN B 229 ASN B 355 HIS B 422 GLN E 229 ASN E 355 HIS E 422 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.065052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.053642 restraints weight = 90060.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.055071 restraints weight = 50667.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.056014 restraints weight = 35494.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.056635 restraints weight = 28450.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.057017 restraints weight = 24711.934| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.113 20727 Z= 0.379 Angle : 0.952 13.628 28425 Z= 0.447 Chirality : 0.051 0.368 3582 Planarity : 0.006 0.105 3312 Dihedral : 5.222 21.037 2484 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.43 % Favored : 95.43 % Rotamer: Outliers : 2.69 % Allowed : 6.82 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.14 (0.17), residues: 2256 helix: 1.90 (0.26), residues: 372 sheet: -0.04 (0.19), residues: 699 loop : -0.35 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 585 TYR 0.020 0.003 TYR B 217 PHE 0.025 0.003 PHE E 176 TRP 0.040 0.003 TRP A 69 HIS 0.009 0.002 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00841 / 0.38 (20526) covalent geometry : angle 0.91425 / 0.44 (27867) SS BOND : bond 0.00430 / 0.27 ( 45) SS BOND : angle 1.19728 / 0.80 ( 90) hydrogen bonds : bond 0.05495 / 3.57 ( 705) hydrogen bonds : angle 6.12960 / 4.34 ( 1953) link_ALPHA1-2 : bond 0.00911 / 0.53 ( 6) link_ALPHA1-2 : angle 1.72137 / 1.09 ( 18) link_ALPHA1-3 : bond 0.00639 / 0.42 ( 21) link_ALPHA1-3 : angle 1.57220 / 1.09 ( 63) link_ALPHA1-6 : bond 0.00599 / 0.33 ( 9) link_ALPHA1-6 : angle 1.76132 / 1.18 ( 27) link_BETA1-4 : bond 0.00553 / 0.34 ( 66) link_BETA1-4 : angle 2.14024 / 1.42 ( 198) link_NAG-ASN : bond 0.00897 / 0.60 ( 54) link_NAG-ASN : angle 2.67113 / 1.82 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 104 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 THR cc_start: 0.7383 (m) cc_final: 0.7129 (p) REVERT: L 29 VAL cc_start: 0.7564 (t) cc_final: 0.6305 (m) REVERT: B 377 ASN cc_start: 0.8477 (t0) cc_final: 0.8185 (t0) REVERT: E 69 TRP cc_start: 0.8610 (m-90) cc_final: 0.7448 (m-10) REVERT: E 100 MET cc_start: 0.8637 (mtp) cc_final: 0.8344 (mtp) REVERT: E 377 ASN cc_start: 0.8513 (t0) cc_final: 0.8232 (t0) REVERT: G 85 ASP cc_start: 0.8991 (p0) cc_final: 0.8745 (p0) outliers start: 54 outliers final: 37 residues processed: 144 average time/residue: 0.1257 time to fit residues: 30.7389 Evaluate side-chains 127 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 90 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 69 MET Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 182 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 124 optimal weight: 0.4980 chunk 216 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 126 optimal weight: 7.9990 chunk 222 optimal weight: 0.0980 chunk 78 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.066197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.054673 restraints weight = 88727.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.056181 restraints weight = 48400.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.057170 restraints weight = 33369.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.057835 restraints weight = 26440.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.058271 restraints weight = 22762.791| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20727 Z= 0.190 Angle : 0.698 7.535 28425 Z= 0.324 Chirality : 0.045 0.263 3582 Planarity : 0.004 0.037 3312 Dihedral : 4.636 19.684 2484 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.84 % Favored : 97.03 % Rotamer: Outliers : 2.09 % Allowed : 8.11 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.18), residues: 2256 helix: 2.19 (0.27), residues: 384 sheet: -0.01 (0.20), residues: 675 loop : -0.48 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 18 TYR 0.020 0.002 TYR F 91 PHE 0.016 0.001 PHE B 383 TRP 0.016 0.002 TRP H 47 HIS 0.004 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (20526) covalent geometry : angle 0.66605 / 0.32 (27867) SS BOND : bond 0.00308 / 0.20 ( 45) SS BOND : angle 0.86606 / 0.57 ( 90) hydrogen bonds : bond 0.04518 / 2.96 ( 705) hydrogen bonds : angle 5.69924 / 4.02 ( 1953) link_ALPHA1-2 : bond 0.00854 / 0.50 ( 6) link_ALPHA1-2 : angle 1.80360 / 1.19 ( 18) link_ALPHA1-3 : bond 0.00641 / 0.41 ( 21) link_ALPHA1-3 : angle 1.38038 / 0.96 ( 63) link_ALPHA1-6 : bond 0.00776 / 0.42 ( 9) link_ALPHA1-6 : angle 1.61219 / 1.10 ( 27) link_BETA1-4 : bond 0.00448 / 0.30 ( 66) link_BETA1-4 : angle 1.79445 / 1.19 ( 198) link_NAG-ASN : bond 0.00380 / 0.25 ( 54) link_NAG-ASN : angle 1.78026 / 1.24 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 103 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 THR cc_start: 0.7414 (m) cc_final: 0.7157 (p) REVERT: H 69 MET cc_start: 0.8585 (mtt) cc_final: 0.8307 (mtt) REVERT: B 377 ASN cc_start: 0.8362 (t0) cc_final: 0.8059 (t0) REVERT: D 69 MET cc_start: 0.8167 (mtm) cc_final: 0.7958 (mtm) REVERT: E 69 TRP cc_start: 0.8573 (m-90) cc_final: 0.7393 (m-10) REVERT: E 100 MET cc_start: 0.8711 (mtp) cc_final: 0.8372 (mtp) REVERT: E 377 ASN cc_start: 0.8476 (t0) cc_final: 0.8172 (t0) REVERT: E 475 MET cc_start: 0.7895 (mmt) cc_final: 0.7513 (mmt) outliers start: 42 outliers final: 30 residues processed: 136 average time/residue: 0.1236 time to fit residues: 28.5393 Evaluate side-chains 119 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 90 GLN Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 185 optimal weight: 3.9990 chunk 202 optimal weight: 0.0050 chunk 22 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 109 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.065544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.054375 restraints weight = 88587.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.055800 restraints weight = 50021.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.056751 restraints weight = 35026.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.057385 restraints weight = 27962.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.057681 restraints weight = 24191.220| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 20727 Z= 0.211 Angle : 0.710 7.571 28425 Z= 0.327 Chirality : 0.045 0.262 3582 Planarity : 0.004 0.036 3312 Dihedral : 4.624 20.085 2484 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.26 % Favored : 95.61 % Rotamer: Outliers : 2.39 % Allowed : 8.41 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.11 (0.18), residues: 2256 helix: 2.33 (0.27), residues: 384 sheet: -0.06 (0.20), residues: 624 loop : -0.55 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 18 TYR 0.018 0.002 TYR E 638 PHE 0.018 0.002 PHE E 522 TRP 0.009 0.001 TRP A 427 HIS 0.004 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (20526) covalent geometry : angle 0.67835 / 0.32 (27867) SS BOND : bond 0.00272 / 0.18 ( 45) SS BOND : angle 0.78726 / 0.52 ( 90) hydrogen bonds : bond 0.04371 / 2.86 ( 705) hydrogen bonds : angle 5.57149 / 3.91 ( 1953) link_ALPHA1-2 : bond 0.00844 / 0.48 ( 6) link_ALPHA1-2 : angle 1.81869 / 1.16 ( 18) link_ALPHA1-3 : bond 0.00655 / 0.41 ( 21) link_ALPHA1-3 : angle 1.36306 / 0.96 ( 63) link_ALPHA1-6 : bond 0.00724 / 0.40 ( 9) link_ALPHA1-6 : angle 1.66908 / 1.14 ( 27) link_BETA1-4 : bond 0.00448 / 0.29 ( 66) link_BETA1-4 : angle 1.80831 / 1.20 ( 198) link_NAG-ASN : bond 0.00449 / 0.29 ( 54) link_NAG-ASN : angle 1.85387 / 1.27 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 92 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 377 ASN cc_start: 0.8415 (t0) cc_final: 0.8112 (t0) REVERT: E 69 TRP cc_start: 0.8502 (m-90) cc_final: 0.7450 (m-10) REVERT: E 100 MET cc_start: 0.8581 (mtp) cc_final: 0.8342 (mtp) REVERT: E 104 MET cc_start: 0.9064 (tpp) cc_final: 0.8553 (ttm) REVERT: E 377 ASN cc_start: 0.8472 (t0) cc_final: 0.8160 (t0) REVERT: E 475 MET cc_start: 0.7964 (mmt) cc_final: 0.7712 (mmt) outliers start: 48 outliers final: 37 residues processed: 132 average time/residue: 0.1234 time to fit residues: 27.9543 Evaluate side-chains 120 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 83 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 90 GLN Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 218 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 9 optimal weight: 0.1980 chunk 147 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 69 optimal weight: 0.0870 chunk 13 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.067026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.055907 restraints weight = 88068.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.057372 restraints weight = 49395.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.058349 restraints weight = 34357.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.058983 restraints weight = 27368.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.059356 restraints weight = 23673.233| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20727 Z= 0.112 Angle : 0.616 7.560 28425 Z= 0.281 Chirality : 0.043 0.224 3582 Planarity : 0.004 0.036 3312 Dihedral : 4.219 18.685 2484 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.79 % Favored : 97.07 % Rotamer: Outliers : 1.34 % Allowed : 9.70 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.42 (0.18), residues: 2256 helix: 2.58 (0.27), residues: 390 sheet: 0.19 (0.21), residues: 621 loop : -0.39 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 18 TYR 0.018 0.001 TYR E 638 PHE 0.013 0.001 PHE A 383 TRP 0.015 0.001 TRP B 69 HIS 0.004 0.001 HIS H 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (20526) covalent geometry : angle 0.58526 / 0.27 (27867) SS BOND : bond 0.00226 / 0.15 ( 45) SS BOND : angle 0.68790 / 0.46 ( 90) hydrogen bonds : bond 0.03823 / 2.52 ( 705) hydrogen bonds : angle 5.25969 / 3.67 ( 1953) link_ALPHA1-2 : bond 0.00803 / 0.46 ( 6) link_ALPHA1-2 : angle 1.80420 / 1.18 ( 18) link_ALPHA1-3 : bond 0.00726 / 0.44 ( 21) link_ALPHA1-3 : angle 1.42465 / 1.00 ( 63) link_ALPHA1-6 : bond 0.00811 / 0.45 ( 9) link_ALPHA1-6 : angle 1.52167 / 1.03 ( 27) link_BETA1-4 : bond 0.00469 / 0.31 ( 66) link_BETA1-4 : angle 1.70197 / 1.13 ( 198) link_NAG-ASN : bond 0.00344 / 0.25 ( 54) link_NAG-ASN : angle 1.50787 / 1.08 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.8298 (m-10) cc_final: 0.7858 (m-10) REVERT: B 377 ASN cc_start: 0.8353 (t0) cc_final: 0.8086 (t0) REVERT: E 69 TRP cc_start: 0.8540 (m-90) cc_final: 0.7587 (m-10) REVERT: E 100 MET cc_start: 0.8665 (mtp) cc_final: 0.8336 (mtp) REVERT: E 377 ASN cc_start: 0.8316 (t0) cc_final: 0.8003 (t0) outliers start: 27 outliers final: 20 residues processed: 127 average time/residue: 0.1224 time to fit residues: 26.7334 Evaluate side-chains 107 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 30 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 80 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 88 optimal weight: 0.0870 chunk 164 optimal weight: 3.9990 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.065720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.054479 restraints weight = 88766.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.055906 restraints weight = 50319.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.056845 restraints weight = 35307.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.057472 restraints weight = 28312.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.057842 restraints weight = 24553.511| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20727 Z= 0.204 Angle : 0.685 7.576 28425 Z= 0.312 Chirality : 0.044 0.254 3582 Planarity : 0.004 0.035 3312 Dihedral : 4.414 18.096 2484 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.21 % Favored : 95.66 % Rotamer: Outliers : 2.09 % Allowed : 9.85 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.18), residues: 2256 helix: 2.51 (0.27), residues: 390 sheet: 0.02 (0.21), residues: 609 loop : -0.42 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 38 TYR 0.012 0.002 TYR C 49 PHE 0.015 0.001 PHE B 383 TRP 0.011 0.001 TRP B 628 HIS 0.003 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (20526) covalent geometry : angle 0.65273 / 0.31 (27867) SS BOND : bond 0.00256 / 0.17 ( 45) SS BOND : angle 0.72850 / 0.49 ( 90) hydrogen bonds : bond 0.04077 / 2.67 ( 705) hydrogen bonds : angle 5.33759 / 3.73 ( 1953) link_ALPHA1-2 : bond 0.00831 / 0.47 ( 6) link_ALPHA1-2 : angle 1.78079 / 1.15 ( 18) link_ALPHA1-3 : bond 0.00658 / 0.41 ( 21) link_ALPHA1-3 : angle 1.38641 / 0.97 ( 63) link_ALPHA1-6 : bond 0.00694 / 0.38 ( 9) link_ALPHA1-6 : angle 1.61436 / 1.10 ( 27) link_BETA1-4 : bond 0.00446 / 0.29 ( 66) link_BETA1-4 : angle 1.78749 / 1.19 ( 198) link_NAG-ASN : bond 0.00426 / 0.29 ( 54) link_NAG-ASN : angle 1.79395 / 1.24 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 86 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.8384 (m-10) cc_final: 0.7652 (m-10) REVERT: B 209 THR cc_start: 0.7139 (m) cc_final: 0.6810 (p) REVERT: E 100 MET cc_start: 0.8566 (mtp) cc_final: 0.8356 (mtp) REVERT: E 104 MET cc_start: 0.9059 (tpp) cc_final: 0.8619 (ttm) outliers start: 42 outliers final: 34 residues processed: 122 average time/residue: 0.1193 time to fit residues: 25.4552 Evaluate side-chains 118 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 84 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 90 GLN Chi-restraints excluded: chain G residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 121 optimal weight: 5.9990 chunk 46 optimal weight: 0.4980 chunk 154 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 95 optimal weight: 0.0170 chunk 178 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.066903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.055786 restraints weight = 87821.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.057244 restraints weight = 49315.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.058201 restraints weight = 34376.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.058847 restraints weight = 27422.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.059248 restraints weight = 23714.449| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 20727 Z= 0.108 Angle : 0.611 8.136 28425 Z= 0.276 Chirality : 0.043 0.216 3582 Planarity : 0.004 0.035 3312 Dihedral : 4.133 17.370 2484 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.24 % Favored : 96.72 % Rotamer: Outliers : 1.64 % Allowed : 10.55 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.18), residues: 2256 helix: 2.67 (0.27), residues: 390 sheet: 0.21 (0.21), residues: 603 loop : -0.38 (0.18), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 18 TYR 0.010 0.001 TYR B 638 PHE 0.013 0.001 PHE E 383 TRP 0.012 0.001 TRP A 69 HIS 0.003 0.001 HIS H 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (20526) covalent geometry : angle 0.58082 / 0.27 (27867) SS BOND : bond 0.00204 / 0.13 ( 45) SS BOND : angle 0.64096 / 0.43 ( 90) hydrogen bonds : bond 0.03664 / 2.42 ( 705) hydrogen bonds : angle 5.11182 / 3.57 ( 1953) link_ALPHA1-2 : bond 0.00854 / 0.48 ( 6) link_ALPHA1-2 : angle 1.77182 / 1.15 ( 18) link_ALPHA1-3 : bond 0.00718 / 0.44 ( 21) link_ALPHA1-3 : angle 1.43166 / 1.00 ( 63) link_ALPHA1-6 : bond 0.00787 / 0.44 ( 9) link_ALPHA1-6 : angle 1.50677 / 1.01 ( 27) link_BETA1-4 : bond 0.00461 / 0.30 ( 66) link_BETA1-4 : angle 1.69924 / 1.13 ( 198) link_NAG-ASN : bond 0.00283 / 0.20 ( 54) link_NAG-ASN : angle 1.51035 / 1.08 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.8336 (m-10) cc_final: 0.7893 (m-10) REVERT: B 209 THR cc_start: 0.7267 (m) cc_final: 0.6925 (p) REVERT: B 530 MET cc_start: 0.8113 (tpp) cc_final: 0.7906 (tpp) REVERT: B 571 TRP cc_start: 0.7702 (m100) cc_final: 0.7297 (m100) REVERT: E 69 TRP cc_start: 0.8297 (m-90) cc_final: 0.7368 (m-10) REVERT: E 100 MET cc_start: 0.8661 (mtp) cc_final: 0.8332 (mtp) REVERT: E 475 MET cc_start: 0.7738 (mmt) cc_final: 0.7439 (mmt) REVERT: G 53 ASN cc_start: 0.8654 (m-40) cc_final: 0.8404 (m-40) outliers start: 33 outliers final: 29 residues processed: 123 average time/residue: 0.1203 time to fit residues: 25.7152 Evaluate side-chains 117 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 90 GLN Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 42 optimal weight: 6.9990 chunk 89 optimal weight: 0.0870 chunk 106 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.065552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.054370 restraints weight = 87425.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.055827 restraints weight = 47665.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.056815 restraints weight = 32678.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.057452 restraints weight = 25804.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.057871 restraints weight = 22213.523| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20727 Z= 0.195 Angle : 0.687 9.685 28425 Z= 0.311 Chirality : 0.045 0.248 3582 Planarity : 0.004 0.036 3312 Dihedral : 4.359 20.880 2484 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.39 % Rotamer: Outliers : 2.04 % Allowed : 10.40 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.29 (0.18), residues: 2256 helix: 2.59 (0.26), residues: 390 sheet: -0.02 (0.21), residues: 609 loop : -0.44 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 38 TYR 0.027 0.002 TYR E 638 PHE 0.014 0.001 PHE B 383 TRP 0.012 0.001 TRP B 628 HIS 0.003 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (20526) covalent geometry : angle 0.65595 / 0.30 (27867) SS BOND : bond 0.00236 / 0.16 ( 45) SS BOND : angle 0.69797 / 0.47 ( 90) hydrogen bonds : bond 0.03925 / 2.56 ( 705) hydrogen bonds : angle 5.23117 / 3.66 ( 1953) link_ALPHA1-2 : bond 0.00856 / 0.49 ( 6) link_ALPHA1-2 : angle 1.77731 / 1.14 ( 18) link_ALPHA1-3 : bond 0.00649 / 0.41 ( 21) link_ALPHA1-3 : angle 1.40565 / 0.98 ( 63) link_ALPHA1-6 : bond 0.00678 / 0.38 ( 9) link_ALPHA1-6 : angle 1.59277 / 1.07 ( 27) link_BETA1-4 : bond 0.00434 / 0.28 ( 66) link_BETA1-4 : angle 1.79243 / 1.20 ( 198) link_NAG-ASN : bond 0.00486 / 0.35 ( 54) link_NAG-ASN : angle 1.77891 / 1.27 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 84 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.8414 (m-10) cc_final: 0.7644 (m-10) REVERT: B 209 THR cc_start: 0.7389 (m) cc_final: 0.7021 (p) REVERT: E 100 MET cc_start: 0.8667 (mtp) cc_final: 0.8422 (mtp) REVERT: E 104 MET cc_start: 0.9103 (tpp) cc_final: 0.8686 (ttm) outliers start: 41 outliers final: 35 residues processed: 119 average time/residue: 0.1207 time to fit residues: 24.9616 Evaluate side-chains 117 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 90 GLN Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 102 optimal weight: 8.9990 chunk 179 optimal weight: 1.9990 chunk 21 optimal weight: 0.0040 chunk 213 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 114 optimal weight: 0.0370 chunk 101 optimal weight: 1.9990 chunk 222 optimal weight: 0.2980 chunk 35 optimal weight: 0.9990 overall best weight: 0.4472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.067167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.055881 restraints weight = 87801.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.057398 restraints weight = 47914.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.058405 restraints weight = 32803.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.059053 restraints weight = 25952.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.059485 restraints weight = 22382.409| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 20727 Z= 0.103 Angle : 0.617 10.083 28425 Z= 0.276 Chirality : 0.043 0.205 3582 Planarity : 0.004 0.037 3312 Dihedral : 4.081 19.682 2484 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.68 % Rotamer: Outliers : 1.49 % Allowed : 11.00 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.48 (0.18), residues: 2256 helix: 2.74 (0.27), residues: 390 sheet: 0.09 (0.20), residues: 681 loop : -0.32 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 18 TYR 0.011 0.001 TYR B 638 PHE 0.012 0.001 PHE A 383 TRP 0.024 0.001 TRP D 36 HIS 0.003 0.001 HIS G 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (20526) covalent geometry : angle 0.58666 / 0.27 (27867) SS BOND : bond 0.00189 / 0.12 ( 45) SS BOND : angle 0.66922 / 0.44 ( 90) hydrogen bonds : bond 0.03556 / 2.34 ( 705) hydrogen bonds : angle 5.01612 / 3.49 ( 1953) link_ALPHA1-2 : bond 0.00837 / 0.47 ( 6) link_ALPHA1-2 : angle 1.76121 / 1.13 ( 18) link_ALPHA1-3 : bond 0.00724 / 0.44 ( 21) link_ALPHA1-3 : angle 1.44273 / 1.01 ( 63) link_ALPHA1-6 : bond 0.00781 / 0.43 ( 9) link_ALPHA1-6 : angle 1.48097 / 0.99 ( 27) link_BETA1-4 : bond 0.00466 / 0.30 ( 66) link_BETA1-4 : angle 1.69013 / 1.13 ( 198) link_NAG-ASN : bond 0.00356 / 0.27 ( 54) link_NAG-ASN : angle 1.49368 / 1.09 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7799 (mmt) cc_final: 0.7401 (mmt) REVERT: A 530 MET cc_start: 0.7464 (tpp) cc_final: 0.7198 (tpp) REVERT: L 87 TYR cc_start: 0.8116 (m-80) cc_final: 0.7711 (m-80) REVERT: B 69 TRP cc_start: 0.8308 (m-10) cc_final: 0.7969 (m-10) REVERT: B 209 THR cc_start: 0.7258 (m) cc_final: 0.6954 (p) REVERT: E 69 TRP cc_start: 0.8276 (m-90) cc_final: 0.7399 (m-10) REVERT: E 100 MET cc_start: 0.8673 (mtp) cc_final: 0.8373 (mtp) REVERT: E 104 MET cc_start: 0.9061 (tpp) cc_final: 0.8622 (ttm) REVERT: E 415 MET cc_start: 0.7575 (ppp) cc_final: 0.7249 (ppp) REVERT: E 475 MET cc_start: 0.8046 (mmt) cc_final: 0.7829 (mmt) REVERT: G 53 ASN cc_start: 0.8669 (m-40) cc_final: 0.8432 (m-40) outliers start: 30 outliers final: 27 residues processed: 119 average time/residue: 0.1148 time to fit residues: 23.9730 Evaluate side-chains 116 residues out of total 2010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 174 optimal weight: 0.6980 chunk 115 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 205 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 84 optimal weight: 0.0870 chunk 208 optimal weight: 6.9990 chunk 79 optimal weight: 0.0570 chunk 214 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.067177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.056025 restraints weight = 87043.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.057562 restraints weight = 46625.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.058567 restraints weight = 31600.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.059227 restraints weight = 24769.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.059648 restraints weight = 21224.539| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 20727 Z= 0.102 Angle : 0.608 9.725 28425 Z= 0.271 Chirality : 0.043 0.209 3582 Planarity : 0.004 0.037 3312 Dihedral : 3.968 19.299 2484 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.24 % Favored : 96.72 % Rotamer: Outliers : 1.59 % Allowed : 10.95 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.56 (0.18), residues: 2256 helix: 2.56 (0.27), residues: 408 sheet: 0.15 (0.20), residues: 681 loop : -0.22 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 18 TYR 0.014 0.001 TYR L 49 PHE 0.012 0.001 PHE A 383 TRP 0.041 0.001 TRP D 36 HIS 0.003 0.001 HIS H 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (20526) covalent geometry : angle 0.57701 / 0.26 (27867) SS BOND : bond 0.00176 / 0.11 ( 45) SS BOND : angle 0.63654 / 0.42 ( 90) hydrogen bonds : bond 0.03404 / 2.26 ( 705) hydrogen bonds : angle 4.91396 / 3.42 ( 1953) link_ALPHA1-2 : bond 0.00855 / 0.48 ( 6) link_ALPHA1-2 : angle 1.70911 / 1.09 ( 18) link_ALPHA1-3 : bond 0.00709 / 0.43 ( 21) link_ALPHA1-3 : angle 1.42661 / 0.99 ( 63) link_ALPHA1-6 : bond 0.00755 / 0.42 ( 9) link_ALPHA1-6 : angle 1.43582 / 0.95 ( 27) link_BETA1-4 : bond 0.00449 / 0.29 ( 66) link_BETA1-4 : angle 1.68930 / 1.13 ( 198) link_NAG-ASN : bond 0.00298 / 0.22 ( 54) link_NAG-ASN : angle 1.57668 / 1.19 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2627.81 seconds wall clock time: 47 minutes 5.19 seconds (2825.19 seconds total)