Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 06:02:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jfo_22308/05_2023/7jfo_22308_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jfo_22308/05_2023/7jfo_22308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jfo_22308/05_2023/7jfo_22308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jfo_22308/05_2023/7jfo_22308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jfo_22308/05_2023/7jfo_22308_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jfo_22308/05_2023/7jfo_22308_updated.pdb" } resolution = 2.13 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 ------------------------------------------------------------------------------- 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= 0.019 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 280 5.16 5 C 23904 2.51 5 N 6680 2.21 5 O 8094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 125": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "D PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 125": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 187": "NH1" <-> "NH2" Residue "E PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 305": "NH1" <-> "NH2" Residue "E PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 360": "NH1" <-> "NH2" Residue "F PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 13": "OE1" <-> "OE2" Residue "F TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 125": "NH1" <-> "NH2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G ARG 79": "NH1" <-> "NH2" Residue "G TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 131": "NH1" <-> "NH2" Residue "G ARG 187": "NH1" <-> "NH2" Residue "G PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 305": "NH1" <-> "NH2" Residue "G PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 360": "NH1" <-> "NH2" Residue "H PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 125": "NH1" <-> "NH2" Residue "I ARG 21": "NH1" <-> "NH2" Residue "I ARG 79": "NH1" <-> "NH2" Residue "I TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 131": "NH1" <-> "NH2" Residue "I ARG 187": "NH1" <-> "NH2" Residue "I PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 305": "NH1" <-> "NH2" Residue "I PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 360": "NH1" <-> "NH2" Residue "J PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 84": "NH1" <-> "NH2" Residue "J TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 125": "NH1" <-> "NH2" Residue "K ARG 21": "NH1" <-> "NH2" Residue "K ARG 79": "NH1" <-> "NH2" Residue "K TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 131": "NH1" <-> "NH2" Residue "K ARG 187": "NH1" <-> "NH2" Residue "K PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 305": "NH1" <-> "NH2" Residue "K PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 360": "NH1" <-> "NH2" Residue "L PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 13": "OE1" <-> "OE2" Residue "L TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 84": "NH1" <-> "NH2" Residue "L ARG 91": "NH1" <-> "NH2" Residue "L TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 125": "NH1" <-> "NH2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 79": "NH1" <-> "NH2" Residue "M TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 131": "NH1" <-> "NH2" Residue "M ARG 187": "NH1" <-> "NH2" Residue "M PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 305": "NH1" <-> "NH2" Residue "M PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 360": "NH1" <-> "NH2" Residue "N PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 84": "NH1" <-> "NH2" Residue "N ARG 91": "NH1" <-> "NH2" Residue "N TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 125": "NH1" <-> "NH2" Residue "O ARG 21": "NH1" <-> "NH2" Residue "O ARG 79": "NH1" <-> "NH2" Residue "O TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 131": "NH1" <-> "NH2" Residue "O ARG 187": "NH1" <-> "NH2" Residue "O PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 305": "NH1" <-> "NH2" Residue "O PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 360": "NH1" <-> "NH2" Residue "P PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 84": "NH1" <-> "NH2" Residue "P ARG 91": "NH1" <-> "NH2" Residue "P TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 125": "NH1" <-> "NH2" Residue "r GLU 68": "OE1" <-> "OE2" Residue "r ARG 71": "NH1" <-> "NH2" Residue "s GLU 68": "OE1" <-> "OE2" Residue "s ARG 71": "NH1" <-> "NH2" Residue "t GLU 68": "OE1" <-> "OE2" Residue "t ARG 71": "NH1" <-> "NH2" Residue "u GLU 68": "OE1" <-> "OE2" Residue "u ARG 71": "NH1" <-> "NH2" Residue "v ARG 71": "NH1" <-> "NH2" Residue "w GLU 68": "OE1" <-> "OE2" Residue "w ARG 71": "NH1" <-> "NH2" Residue "x GLU 68": "OE1" <-> "OE2" Residue "x ARG 71": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 38958 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "C" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "E" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "F" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "G" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "H" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "I" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "J" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "K" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "L" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "M" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "N" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "O" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "P" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "q" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "r" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "s" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "t" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "u" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "v" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "w" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "x" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 108 Classifications: {'water': 108} Link IDs: {None: 107} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "C" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "E" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "F" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "G" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "I" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "J" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "K" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "L" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "M" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "N" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "O" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 108 Classifications: {'water': 108} Link IDs: {None: 107} Chain: "P" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Time building chain proxies: 19.63, per 1000 atoms: 0.50 Number of scatterers: 38958 At special positions: 0 Unit cell: (142.135, 142.135, 139.515, 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 280 16.00 O 8094 8.00 N 6680 7.00 C 23904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Time building additional restraints: 17.47 Conformation dependent library (CDL) restraints added in 5.7 seconds 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 200 helices and 32 sheets defined 38.9% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 50 through 59 Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 113 through 121 Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 142 through 147 removed outlier: 4.229A pdb=" N THR A 147 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 214 through 232 Processing helix chain 'A' and resid 247 through 258 Processing helix chain 'A' and resid 269 through 272 No H-bonds generated for 'chain 'A' and resid 269 through 272' Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'A' and resid 336 through 350 Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 387 through 394 Processing helix chain 'A' and resid 405 through 408 No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 413 through 432 Processing helix chain 'A' and resid 437 through 451 removed outlier: 6.358A pdb=" N GLY A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASP A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TRP A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 460 Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 47 through 50 No H-bonds generated for 'chain 'B' and resid 47 through 50' Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'C' and resid 50 through 59 Processing helix chain 'C' and resid 105 through 107 No H-bonds generated for 'chain 'C' and resid 105 through 107' Processing helix chain 'C' and resid 113 through 121 Processing helix chain 'C' and resid 124 through 126 No H-bonds generated for 'chain 'C' and resid 124 through 126' Processing helix chain 'C' and resid 142 through 147 removed outlier: 4.225A pdb=" N THR C 147 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 182 through 194 Processing helix chain 'C' and resid 214 through 232 Processing helix chain 'C' and resid 247 through 258 Processing helix chain 'C' and resid 269 through 272 No H-bonds generated for 'chain 'C' and resid 269 through 272' Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 298 through 302 Processing helix chain 'C' and resid 311 through 321 Processing helix chain 'C' and resid 336 through 350 Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 387 through 394 Processing helix chain 'C' and resid 405 through 408 No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 413 through 432 Processing helix chain 'C' and resid 437 through 451 removed outlier: 6.348A pdb=" N GLY C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS C 450 " --> pdb=" O ARG C 446 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TRP C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 460 Processing helix chain 'D' and resid 23 through 35 Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 86 through 99 Processing helix chain 'E' and resid 50 through 59 Processing helix chain 'E' and resid 105 through 107 No H-bonds generated for 'chain 'E' and resid 105 through 107' Processing helix chain 'E' and resid 113 through 121 Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 142 through 147 removed outlier: 4.225A pdb=" N THR E 147 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 Processing helix chain 'E' and resid 182 through 194 Processing helix chain 'E' and resid 214 through 232 Processing helix chain 'E' and resid 247 through 258 Processing helix chain 'E' and resid 269 through 272 No H-bonds generated for 'chain 'E' and resid 269 through 272' Processing helix chain 'E' and resid 274 through 287 Processing helix chain 'E' and resid 298 through 302 Processing helix chain 'E' and resid 311 through 321 Processing helix chain 'E' and resid 336 through 350 Processing helix chain 'E' and resid 358 through 360 No H-bonds generated for 'chain 'E' and resid 358 through 360' Processing helix chain 'E' and resid 387 through 394 Processing helix chain 'E' and resid 405 through 408 No H-bonds generated for 'chain 'E' and resid 405 through 408' Processing helix chain 'E' and resid 413 through 432 Processing helix chain 'E' and resid 437 through 451 removed outlier: 6.385A pdb=" N GLY E 442 " --> pdb=" O ALA E 438 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASP E 443 " --> pdb=" O ARG E 439 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TRP E 451 " --> pdb=" O SER E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 460 Processing helix chain 'F' and resid 23 through 35 Processing helix chain 'F' and resid 47 through 50 No H-bonds generated for 'chain 'F' and resid 47 through 50' Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 86 through 99 Processing helix chain 'G' and resid 50 through 59 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 124 through 126 No H-bonds generated for 'chain 'G' and resid 124 through 126' Processing helix chain 'G' and resid 142 through 147 removed outlier: 4.217A pdb=" N THR G 147 " --> pdb=" O ALA G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 162 Processing helix chain 'G' and resid 182 through 194 Processing helix chain 'G' and resid 214 through 232 Processing helix chain 'G' and resid 247 through 258 Processing helix chain 'G' and resid 269 through 272 No H-bonds generated for 'chain 'G' and resid 269 through 272' Processing helix chain 'G' and resid 274 through 287 Processing helix chain 'G' and resid 298 through 302 Processing helix chain 'G' and resid 311 through 321 Processing helix chain 'G' and resid 336 through 350 Processing helix chain 'G' and resid 358 through 360 No H-bonds generated for 'chain 'G' and resid 358 through 360' Processing helix chain 'G' and resid 387 through 394 Processing helix chain 'G' and resid 405 through 408 No H-bonds generated for 'chain 'G' and resid 405 through 408' Processing helix chain 'G' and resid 413 through 432 Processing helix chain 'G' and resid 437 through 451 removed outlier: 6.377A pdb=" N GLY G 442 " --> pdb=" O ALA G 438 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ASP G 443 " --> pdb=" O ARG G 439 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TRP G 451 " --> pdb=" O SER G 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 453 through 460 Processing helix chain 'H' and resid 23 through 35 Processing helix chain 'H' and resid 47 through 50 No H-bonds generated for 'chain 'H' and resid 47 through 50' Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'H' and resid 86 through 99 Processing helix chain 'I' and resid 50 through 59 Processing helix chain 'I' and resid 105 through 107 No H-bonds generated for 'chain 'I' and resid 105 through 107' Processing helix chain 'I' and resid 113 through 121 Processing helix chain 'I' and resid 124 through 126 No H-bonds generated for 'chain 'I' and resid 124 through 126' Processing helix chain 'I' and resid 142 through 147 removed outlier: 4.217A pdb=" N THR I 147 " --> pdb=" O ALA I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 162 Processing helix chain 'I' and resid 182 through 194 Processing helix chain 'I' and resid 214 through 232 Processing helix chain 'I' and resid 247 through 258 Processing helix chain 'I' and resid 269 through 272 No H-bonds generated for 'chain 'I' and resid 269 through 272' Processing helix chain 'I' and resid 274 through 287 Processing helix chain 'I' and resid 298 through 302 Processing helix chain 'I' and resid 311 through 321 Processing helix chain 'I' and resid 336 through 350 Processing helix chain 'I' and resid 358 through 360 No H-bonds generated for 'chain 'I' and resid 358 through 360' Processing helix chain 'I' and resid 387 through 394 Processing helix chain 'I' and resid 405 through 408 No H-bonds generated for 'chain 'I' and resid 405 through 408' Processing helix chain 'I' and resid 413 through 432 Processing helix chain 'I' and resid 437 through 451 removed outlier: 6.378A pdb=" N GLY I 442 " --> pdb=" O ALA I 438 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASP I 443 " --> pdb=" O ARG I 439 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TRP I 451 " --> pdb=" O SER I 447 " (cutoff:3.500A) Processing helix chain 'I' and resid 453 through 460 Processing helix chain 'J' and resid 23 through 35 Processing helix chain 'J' and resid 47 through 50 No H-bonds generated for 'chain 'J' and resid 47 through 50' Processing helix chain 'J' and resid 55 through 59 Processing helix chain 'J' and resid 86 through 99 Processing helix chain 'K' and resid 50 through 59 Processing helix chain 'K' and resid 105 through 107 No H-bonds generated for 'chain 'K' and resid 105 through 107' Processing helix chain 'K' and resid 113 through 121 Processing helix chain 'K' and resid 124 through 126 No H-bonds generated for 'chain 'K' and resid 124 through 126' Processing helix chain 'K' and resid 142 through 147 removed outlier: 4.232A pdb=" N THR K 147 " --> pdb=" O ALA K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 162 Processing helix chain 'K' and resid 182 through 194 Processing helix chain 'K' and resid 214 through 232 Processing helix chain 'K' and resid 247 through 258 Processing helix chain 'K' and resid 269 through 272 No H-bonds generated for 'chain 'K' and resid 269 through 272' Processing helix chain 'K' and resid 274 through 287 Processing helix chain 'K' and resid 298 through 302 Processing helix chain 'K' and resid 311 through 321 Processing helix chain 'K' and resid 336 through 350 Processing helix chain 'K' and resid 358 through 360 No H-bonds generated for 'chain 'K' and resid 358 through 360' Processing helix chain 'K' and resid 387 through 394 Processing helix chain 'K' and resid 405 through 408 No H-bonds generated for 'chain 'K' and resid 405 through 408' Processing helix chain 'K' and resid 413 through 432 Processing helix chain 'K' and resid 437 through 451 removed outlier: 6.409A pdb=" N GLY K 442 " --> pdb=" O ALA K 438 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASP K 443 " --> pdb=" O ARG K 439 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS K 450 " --> pdb=" O ARG K 446 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP K 451 " --> pdb=" O SER K 447 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 460 Processing helix chain 'L' and resid 23 through 35 Processing helix chain 'L' and resid 47 through 50 No H-bonds generated for 'chain 'L' and resid 47 through 50' Processing helix chain 'L' and resid 55 through 59 Processing helix chain 'L' and resid 86 through 99 Processing helix chain 'M' and resid 50 through 59 Processing helix chain 'M' and resid 105 through 107 No H-bonds generated for 'chain 'M' and resid 105 through 107' Processing helix chain 'M' and resid 113 through 121 Processing helix chain 'M' and resid 124 through 126 No H-bonds generated for 'chain 'M' and resid 124 through 126' Processing helix chain 'M' and resid 142 through 147 removed outlier: 4.232A pdb=" N THR M 147 " --> pdb=" O ALA M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 162 Processing helix chain 'M' and resid 182 through 194 Processing helix chain 'M' and resid 214 through 232 Processing helix chain 'M' and resid 247 through 258 Processing helix chain 'M' and resid 269 through 272 No H-bonds generated for 'chain 'M' and resid 269 through 272' Processing helix chain 'M' and resid 274 through 287 Processing helix chain 'M' and resid 298 through 302 Processing helix chain 'M' and resid 311 through 321 Processing helix chain 'M' and resid 336 through 350 Processing helix chain 'M' and resid 358 through 360 No H-bonds generated for 'chain 'M' and resid 358 through 360' Processing helix chain 'M' and resid 387 through 394 Processing helix chain 'M' and resid 405 through 408 No H-bonds generated for 'chain 'M' and resid 405 through 408' Processing helix chain 'M' and resid 413 through 432 Processing helix chain 'M' and resid 437 through 451 removed outlier: 6.388A pdb=" N GLY M 442 " --> pdb=" O ALA M 438 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASP M 443 " --> pdb=" O ARG M 439 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TRP M 451 " --> pdb=" O SER M 447 " (cutoff:3.500A) Processing helix chain 'M' and resid 453 through 460 Processing helix chain 'N' and resid 23 through 35 Processing helix chain 'N' and resid 47 through 50 No H-bonds generated for 'chain 'N' and resid 47 through 50' Processing helix chain 'N' and resid 55 through 59 Processing helix chain 'N' and resid 86 through 99 Processing helix chain 'O' and resid 50 through 59 Processing helix chain 'O' and resid 105 through 107 No H-bonds generated for 'chain 'O' and resid 105 through 107' Processing helix chain 'O' and resid 113 through 121 Processing helix chain 'O' and resid 124 through 126 No H-bonds generated for 'chain 'O' and resid 124 through 126' Processing helix chain 'O' and resid 142 through 147 removed outlier: 4.232A pdb=" N THR O 147 " --> pdb=" O ALA O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 154 through 162 Processing helix chain 'O' and resid 182 through 194 Processing helix chain 'O' and resid 214 through 232 Processing helix chain 'O' and resid 247 through 258 Processing helix chain 'O' and resid 269 through 272 No H-bonds generated for 'chain 'O' and resid 269 through 272' Processing helix chain 'O' and resid 274 through 287 Processing helix chain 'O' and resid 298 through 302 Processing helix chain 'O' and resid 311 through 321 Processing helix chain 'O' and resid 336 through 350 Processing helix chain 'O' and resid 358 through 360 No H-bonds generated for 'chain 'O' and resid 358 through 360' Processing helix chain 'O' and resid 387 through 394 Processing helix chain 'O' and resid 405 through 408 No H-bonds generated for 'chain 'O' and resid 405 through 408' Processing helix chain 'O' and resid 413 through 432 Processing helix chain 'O' and resid 437 through 451 removed outlier: 6.349A pdb=" N GLY O 442 " --> pdb=" O ALA O 438 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASP O 443 " --> pdb=" O ARG O 439 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TRP O 451 " --> pdb=" O SER O 447 " (cutoff:3.500A) Processing helix chain 'O' and resid 453 through 460 Processing helix chain 'P' and resid 23 through 35 Processing helix chain 'P' and resid 47 through 50 No H-bonds generated for 'chain 'P' and resid 47 through 50' Processing helix chain 'P' and resid 55 through 59 Processing helix chain 'P' and resid 86 through 99 Processing helix chain 'q' and resid 63 through 71 removed outlier: 3.559A pdb=" N SER q 69 " --> pdb=" O GLN q 65 " (cutoff:3.500A) Processing helix chain 'r' and resid 63 through 71 removed outlier: 3.557A pdb=" N SER r 69 " --> pdb=" O GLN r 65 " (cutoff:3.500A) Processing helix chain 's' and resid 63 through 71 removed outlier: 3.559A pdb=" N SER s 69 " --> pdb=" O GLN s 65 " (cutoff:3.500A) Processing helix chain 't' and resid 63 through 71 removed outlier: 3.559A pdb=" N SER t 69 " --> pdb=" O GLN t 65 " (cutoff:3.500A) Processing helix chain 'u' and resid 63 through 71 removed outlier: 3.559A pdb=" N SER u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) Processing helix chain 'v' and resid 63 through 71 removed outlier: 3.559A pdb=" N SER v 69 " --> pdb=" O GLN v 65 " (cutoff:3.500A) Processing helix chain 'w' and resid 63 through 71 removed outlier: 3.559A pdb=" N SER w 69 " --> pdb=" O GLN w 65 " (cutoff:3.500A) Processing helix chain 'x' and resid 63 through 71 removed outlier: 3.558A pdb=" N SER x 69 " --> pdb=" O GLN x 65 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 132 through 139 removed outlier: 6.737A pdb=" N ALA A 39 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU A 138 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 37 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP A 86 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA A 102 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N CYS A 84 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 237 through 239 removed outlier: 3.660A pdb=" N THR A 173 " --> pdb=" O PHE A 402 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN A 401 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA A 378 " --> pdb=" O GLN A 401 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 264 through 268 removed outlier: 6.235A pdb=" N LEU A 290 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HIS A 267 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS A 292 " --> pdb=" O HIS A 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 74 through 76 removed outlier: 4.649A pdb=" N LEU B 42 " --> pdb=" O TRP B 76 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LEU B 107 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU B 122 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ALA B 109 " --> pdb=" O GLY B 120 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLY B 120 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 132 through 139 removed outlier: 6.734A pdb=" N ALA C 39 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU C 138 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU C 37 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP C 86 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA C 102 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N CYS C 84 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 237 through 239 removed outlier: 3.654A pdb=" N THR C 173 " --> pdb=" O PHE C 402 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLN C 401 " --> pdb=" O PRO C 376 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA C 378 " --> pdb=" O GLN C 401 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 264 through 268 removed outlier: 6.234A pdb=" N LEU C 290 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HIS C 267 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS C 292 " --> pdb=" O HIS C 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 74 through 76 removed outlier: 4.651A pdb=" N LEU D 42 " --> pdb=" O TRP D 76 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU D 107 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU D 122 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ALA D 109 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLY D 120 " --> pdb=" O ALA D 109 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 132 through 139 removed outlier: 6.733A pdb=" N ALA E 39 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU E 138 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU E 37 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP E 86 " --> pdb=" O TYR E 100 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA E 102 " --> pdb=" O CYS E 84 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N CYS E 84 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 237 through 239 removed outlier: 3.673A pdb=" N THR E 173 " --> pdb=" O PHE E 402 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLN E 401 " --> pdb=" O PRO E 376 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA E 378 " --> pdb=" O GLN E 401 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 264 through 268 removed outlier: 6.232A pdb=" N LEU E 290 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N HIS E 267 " --> pdb=" O LEU E 290 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N HIS E 292 " --> pdb=" O HIS E 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 74 through 76 removed outlier: 4.656A pdb=" N LEU F 42 " --> pdb=" O TRP F 76 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU F 107 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU F 122 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ALA F 109 " --> pdb=" O GLY F 120 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLY F 120 " --> pdb=" O ALA F 109 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 132 through 139 removed outlier: 6.732A pdb=" N ALA G 39 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU G 138 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU G 37 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP G 86 " --> pdb=" O TYR G 100 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA G 102 " --> pdb=" O CYS G 84 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N CYS G 84 " --> pdb=" O ALA G 102 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 237 through 239 removed outlier: 3.694A pdb=" N THR G 173 " --> pdb=" O PHE G 402 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLN G 401 " --> pdb=" O PRO G 376 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA G 378 " --> pdb=" O GLN G 401 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 264 through 268 removed outlier: 6.234A pdb=" N LEU G 290 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N HIS G 267 " --> pdb=" O LEU G 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS G 292 " --> pdb=" O HIS G 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'H' and resid 74 through 76 removed outlier: 4.653A pdb=" N LEU H 42 " --> pdb=" O TRP H 76 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU H 107 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU H 122 " --> pdb=" O LEU H 107 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ALA H 109 " --> pdb=" O GLY H 120 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLY H 120 " --> pdb=" O ALA H 109 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 132 through 139 removed outlier: 6.735A pdb=" N ALA I 39 " --> pdb=" O GLU I 136 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU I 138 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU I 37 " --> pdb=" O LEU I 138 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP I 86 " --> pdb=" O TYR I 100 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA I 102 " --> pdb=" O CYS I 84 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N CYS I 84 " --> pdb=" O ALA I 102 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 237 through 239 removed outlier: 3.662A pdb=" N THR I 173 " --> pdb=" O PHE I 402 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN I 401 " --> pdb=" O PRO I 376 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA I 378 " --> pdb=" O GLN I 401 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 264 through 268 removed outlier: 6.232A pdb=" N LEU I 290 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HIS I 267 " --> pdb=" O LEU I 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS I 292 " --> pdb=" O HIS I 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'J' and resid 74 through 76 removed outlier: 4.660A pdb=" N LEU J 42 " --> pdb=" O TRP J 76 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU J 107 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU J 122 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ALA J 109 " --> pdb=" O GLY J 120 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLY J 120 " --> pdb=" O ALA J 109 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 132 through 139 removed outlier: 6.734A pdb=" N ALA K 39 " --> pdb=" O GLU K 136 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU K 138 " --> pdb=" O LEU K 37 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU K 37 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP K 86 " --> pdb=" O TYR K 100 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA K 102 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS K 84 " --> pdb=" O ALA K 102 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 237 through 239 removed outlier: 3.646A pdb=" N THR K 173 " --> pdb=" O PHE K 402 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLN K 401 " --> pdb=" O PRO K 376 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA K 378 " --> pdb=" O GLN K 401 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 264 through 268 removed outlier: 6.235A pdb=" N LEU K 290 " --> pdb=" O ILE K 265 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N HIS K 267 " --> pdb=" O LEU K 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS K 292 " --> pdb=" O HIS K 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'L' and resid 74 through 76 removed outlier: 4.648A pdb=" N LEU L 42 " --> pdb=" O TRP L 76 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU L 107 " --> pdb=" O LEU L 122 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU L 122 " --> pdb=" O LEU L 107 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA L 109 " --> pdb=" O GLY L 120 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLY L 120 " --> pdb=" O ALA L 109 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 132 through 139 removed outlier: 6.737A pdb=" N ALA M 39 " --> pdb=" O GLU M 136 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU M 138 " --> pdb=" O LEU M 37 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU M 37 " --> pdb=" O LEU M 138 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP M 86 " --> pdb=" O TYR M 100 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA M 102 " --> pdb=" O CYS M 84 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N CYS M 84 " --> pdb=" O ALA M 102 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 237 through 239 removed outlier: 3.659A pdb=" N THR M 173 " --> pdb=" O PHE M 402 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLN M 401 " --> pdb=" O PRO M 376 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA M 378 " --> pdb=" O GLN M 401 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 264 through 268 removed outlier: 6.243A pdb=" N LEU M 290 " --> pdb=" O ILE M 265 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HIS M 267 " --> pdb=" O LEU M 290 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS M 292 " --> pdb=" O HIS M 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'N' and resid 74 through 76 removed outlier: 4.645A pdb=" N LEU N 42 " --> pdb=" O TRP N 76 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU N 107 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU N 122 " --> pdb=" O LEU N 107 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ALA N 109 " --> pdb=" O GLY N 120 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLY N 120 " --> pdb=" O ALA N 109 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'O' and resid 132 through 139 removed outlier: 6.740A pdb=" N ALA O 39 " --> pdb=" O GLU O 136 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU O 138 " --> pdb=" O LEU O 37 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU O 37 " --> pdb=" O LEU O 138 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP O 86 " --> pdb=" O TYR O 100 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA O 102 " --> pdb=" O CYS O 84 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N CYS O 84 " --> pdb=" O ALA O 102 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'O' and resid 237 through 239 removed outlier: 3.659A pdb=" N THR O 173 " --> pdb=" O PHE O 402 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLN O 401 " --> pdb=" O PRO O 376 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA O 378 " --> pdb=" O GLN O 401 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'O' and resid 264 through 268 removed outlier: 6.245A pdb=" N LEU O 290 " --> pdb=" O ILE O 265 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N HIS O 267 " --> pdb=" O LEU O 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS O 292 " --> pdb=" O HIS O 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'P' and resid 74 through 76 removed outlier: 4.649A pdb=" N LEU P 42 " --> pdb=" O TRP P 76 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU P 107 " --> pdb=" O LEU P 122 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU P 122 " --> pdb=" O LEU P 107 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ALA P 109 " --> pdb=" O GLY P 120 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLY P 120 " --> pdb=" O ALA P 109 " (cutoff:3.500A) 1398 hydrogen bonds defined for protein. 3999 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: 14.28 Time building geometry restraints manager: 18.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 6506 1.30 - 1.44: 10659 1.44 - 1.58: 20717 1.58 - 1.72: 362 1.72 - 1.86: 428 Bond restraints: 38672 Sorted by residual: bond pdb=" SD MET G 266 " pdb=" CE MET G 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.92e+01 bond pdb=" SD MET E 266 " pdb=" CE MET E 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.91e+01 bond pdb=" SD MET O 266 " pdb=" CE MET O 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.91e+01 bond pdb=" SD MET K 266 " pdb=" CE MET K 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.90e+01 bond pdb=" SD MET M 266 " pdb=" CE MET M 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.90e+01 ... (remaining 38667 not shown) Histogram of bond angle deviations from ideal: 92.55 - 100.97: 75 100.97 - 109.40: 5019 109.40 - 117.83: 22906 117.83 - 126.26: 23669 126.26 - 134.69: 763 Bond angle restraints: 52432 Sorted by residual: angle pdb=" N TRP I 66 " pdb=" CA TRP I 66 " pdb=" C TRP I 66 " ideal model delta sigma weight residual 111.36 123.98 -12.62 1.09e+00 8.42e-01 1.34e+02 angle pdb=" N TRP M 66 " pdb=" CA TRP M 66 " pdb=" C TRP M 66 " ideal model delta sigma weight residual 111.36 123.74 -12.38 1.09e+00 8.42e-01 1.29e+02 angle pdb=" N TRP O 66 " pdb=" CA TRP O 66 " pdb=" C TRP O 66 " ideal model delta sigma weight residual 111.36 123.51 -12.15 1.09e+00 8.42e-01 1.24e+02 angle pdb=" N TRP A 66 " pdb=" CA TRP A 66 " pdb=" C TRP A 66 " ideal model delta sigma weight residual 111.36 119.71 -8.35 1.09e+00 8.42e-01 5.87e+01 angle pdb=" N TRP K 66 " pdb=" CA TRP K 66 " pdb=" C TRP K 66 " ideal model delta sigma weight residual 111.36 119.63 -8.27 1.09e+00 8.42e-01 5.76e+01 ... (remaining 52427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.24: 20504 14.24 - 28.49: 2053 28.49 - 42.73: 324 42.73 - 56.97: 83 56.97 - 71.21: 44 Dihedral angle restraints: 23008 sinusoidal: 9128 harmonic: 13880 Sorted by residual: dihedral pdb=" CA PHE F 60 " pdb=" C PHE F 60 " pdb=" N GLY F 61 " pdb=" CA GLY F 61 " ideal model delta harmonic sigma weight residual 180.00 152.39 27.61 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA PHE H 60 " pdb=" C PHE H 60 " pdb=" N GLY H 61 " pdb=" CA GLY H 61 " ideal model delta harmonic sigma weight residual 180.00 152.45 27.55 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA PHE P 60 " pdb=" C PHE P 60 " pdb=" N GLY P 61 " pdb=" CA GLY P 61 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 23005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 4369 0.114 - 0.228: 945 0.228 - 0.342: 194 0.342 - 0.456: 68 0.456 - 0.569: 8 Chirality restraints: 5584 Sorted by residual: chirality pdb=" CB ILE G 301 " pdb=" CA ILE G 301 " pdb=" CG1 ILE G 301 " pdb=" CG2 ILE G 301 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.57 2.00e-01 2.50e+01 8.11e+00 chirality pdb=" CB ILE K 301 " pdb=" CA ILE K 301 " pdb=" CG1 ILE K 301 " pdb=" CG2 ILE K 301 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.56 2.00e-01 2.50e+01 7.93e+00 chirality pdb=" CB ILE E 301 " pdb=" CA ILE E 301 " pdb=" CG1 ILE E 301 " pdb=" CG2 ILE E 301 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.56 2.00e-01 2.50e+01 7.90e+00 ... (remaining 5581 not shown) Planarity restraints: 6880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS I 153 " 0.066 2.00e-02 2.50e+03 5.82e-02 5.08e+01 pdb=" CG HIS I 153 " -0.102 2.00e-02 2.50e+03 pdb=" ND1 HIS I 153 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS I 153 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 HIS I 153 " -0.014 2.00e-02 2.50e+03 pdb=" NE2 HIS I 153 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 153 " -0.066 2.00e-02 2.50e+03 5.81e-02 5.07e+01 pdb=" CG HIS G 153 " 0.101 2.00e-02 2.50e+03 pdb=" ND1 HIS G 153 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS G 153 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 HIS G 153 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS G 153 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 153 " 0.065 2.00e-02 2.50e+03 5.78e-02 5.02e+01 pdb=" CG HIS E 153 " -0.101 2.00e-02 2.50e+03 pdb=" ND1 HIS E 153 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS E 153 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 HIS E 153 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 HIS E 153 " 0.067 2.00e-02 2.50e+03 ... (remaining 6877 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4106 2.74 - 3.28: 40769 3.28 - 3.82: 75120 3.82 - 4.36: 92924 4.36 - 4.90: 145860 Nonbonded interactions: 358779 Sorted by model distance: nonbonded pdb=" NE2 GLN A 156 " pdb=" OD2 ASP A 160 " model vdw 2.198 2.520 nonbonded pdb=" NE2 GLN G 156 " pdb=" OD2 ASP G 160 " model vdw 2.201 2.520 nonbonded pdb=" NE2 GLN O 156 " pdb=" OD2 ASP O 160 " model vdw 2.203 2.520 nonbonded pdb=" NE2 GLN I 156 " pdb=" OD2 ASP I 160 " model vdw 2.204 2.520 nonbonded pdb=" NE2 GLN C 156 " pdb=" OD2 ASP C 160 " model vdw 2.206 2.520 ... (remaining 358774 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.720 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: 0.040 Extract box with map and model: 15.280 Check model and map are aligned: 0.600 Set scattering table: 0.320 Process input model: 97.190 Find NCS groups from input model: 2.670 Set up NCS constraints: 0.390 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:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 : 0.022 0.162 38672 Z= 1.420 Angle : 1.666 12.619 52432 Z= 0.976 Chirality : 0.109 0.569 5584 Planarity : 0.014 0.064 6880 Dihedral : 12.066 71.215 14144 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.11), residues: 4760 helix: -0.72 (0.10), residues: 1856 sheet: -0.22 (0.20), residues: 752 loop : -0.52 (0.13), residues: 2152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 644 time to evaluate : 4.791 Fit side-chains outliers start: 48 outliers final: 7 residues processed: 682 average time/residue: 1.6840 time to fit residues: 1373.2875 Evaluate side-chains 607 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 600 time to evaluate : 4.041 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 5.6247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 398 optimal weight: 4.9990 chunk 357 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 241 optimal weight: 0.9990 chunk 191 optimal weight: 0.9990 chunk 369 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 chunk 428 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 96 GLN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN A 163 ASN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 HIS A 241 ASN A 267 HIS A 277 ASN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN A 432 ASN B 8 ASN B 9 ASN B 29 GLN B 36 ASN C 45 GLN C 96 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 163 ASN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 HIS C 241 ASN C 267 HIS C 277 ASN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 ASN C 432 ASN D 8 ASN D 9 ASN D 29 GLN D 36 ASN D 124 GLN E 45 GLN E 95 ASN E 96 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 HIS E 241 ASN E 267 HIS E 277 ASN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 420 ASN E 432 ASN F 8 ASN F 9 ASN F 29 GLN F 36 ASN F 124 GLN G 45 GLN G 95 ASN G 96 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN G 163 ASN ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 238 HIS G 241 ASN G 267 HIS G 277 ASN ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 420 ASN G 432 ASN H 8 ASN H 9 ASN H 29 GLN H 36 ASN H 124 GLN I 45 GLN I 96 GLN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 163 ASN ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 238 HIS I 241 ASN I 267 HIS I 277 ASN ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 ASN I 432 ASN J 8 ASN J 9 ASN J 29 GLN J 36 ASN J 124 GLN K 45 GLN K 96 GLN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN K 163 ASN ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 238 HIS K 241 ASN K 267 HIS K 277 ASN ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 420 ASN K 432 ASN L 8 ASN L 9 ASN L 29 GLN L 36 ASN M 45 GLN M 96 GLN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN M 163 ASN ** M 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 238 HIS M 241 ASN M 267 HIS M 277 ASN ** M 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 420 ASN M 432 ASN N 8 ASN N 9 ASN N 29 GLN N 36 ASN N 124 GLN O 45 GLN O 95 ASN O 96 GLN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN O 163 ASN ** O 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 238 HIS O 241 ASN O 267 HIS O 277 ASN ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 420 ASN O 432 ASN P 8 ASN P 9 ASN P 29 GLN P 36 ASN P 124 GLN Total number of N/Q/H flips: 119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 38672 Z= 0.205 Angle : 0.642 5.872 52432 Z= 0.351 Chirality : 0.045 0.181 5584 Planarity : 0.005 0.049 6880 Dihedral : 5.781 24.444 5360 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.12), residues: 4760 helix: 0.93 (0.11), residues: 1864 sheet: 0.15 (0.19), residues: 696 loop : -0.05 (0.13), residues: 2200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 693 time to evaluate : 4.391 Fit side-chains outliers start: 38 outliers final: 18 residues processed: 717 average time/residue: 1.6665 time to fit residues: 1435.0779 Evaluate side-chains 676 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 658 time to evaluate : 4.577 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 2.0198 time to fit residues: 15.4043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 238 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 356 optimal weight: 3.9990 chunk 291 optimal weight: 10.0000 chunk 118 optimal weight: 40.0000 chunk 429 optimal weight: 9.9990 chunk 463 optimal weight: 30.0000 chunk 382 optimal weight: 6.9990 chunk 425 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 344 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 95 ASN A 96 GLN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 45 GLN C 95 ASN C 96 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN D 124 GLN E 45 GLN E 96 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN F 124 GLN G 96 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN H 124 GLN I 95 ASN I 96 GLN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN J 124 GLN K 45 GLN K 95 ASN K 96 GLN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN K 207 ASN ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 45 GLN M 95 ASN M 96 GLN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN ** M 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN N 124 GLN O 45 GLN O 96 GLN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN ** O 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN P 124 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 38672 Z= 0.295 Angle : 0.710 6.087 52432 Z= 0.384 Chirality : 0.049 0.199 5584 Planarity : 0.006 0.057 6880 Dihedral : 5.837 24.105 5360 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.12), residues: 4760 helix: 1.11 (0.12), residues: 1920 sheet: 0.20 (0.19), residues: 696 loop : -0.02 (0.14), residues: 2144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 651 time to evaluate : 4.520 Fit side-chains outliers start: 39 outliers final: 20 residues processed: 678 average time/residue: 1.7425 time to fit residues: 1411.6705 Evaluate side-chains 662 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 642 time to evaluate : 4.220 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 20 residues processed: 0 time to fit residues: 5.9012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 424 optimal weight: 3.9990 chunk 322 optimal weight: 2.9990 chunk 222 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 288 optimal weight: 4.9990 chunk 430 optimal weight: 0.0370 chunk 456 optimal weight: 20.0000 chunk 225 optimal weight: 10.0000 chunk 408 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN A 207 ASN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 96 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 207 ASN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 96 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN E 207 ASN ** E 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 96 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN G 207 ASN ** G 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN I 96 GLN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN I 207 ASN ** I 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 96 GLN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN M 207 ASN ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 96 GLN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN O 207 ASN ** O 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 38672 Z= 0.248 Angle : 0.657 5.855 52432 Z= 0.355 Chirality : 0.047 0.190 5584 Planarity : 0.005 0.056 6880 Dihedral : 5.674 23.478 5360 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.12), residues: 4760 helix: 1.48 (0.12), residues: 1872 sheet: 0.17 (0.19), residues: 696 loop : 0.05 (0.14), residues: 2192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 659 time to evaluate : 4.412 Fit side-chains outliers start: 52 outliers final: 28 residues processed: 690 average time/residue: 1.7032 time to fit residues: 1405.4227 Evaluate side-chains 677 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 649 time to evaluate : 4.641 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 28 residues processed: 0 time to fit residues: 5.8804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 379 optimal weight: 5.9990 chunk 258 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 339 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 389 optimal weight: 9.9990 chunk 315 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 232 optimal weight: 30.0000 chunk 409 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 96 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 96 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 96 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN H 124 GLN I 96 GLN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 96 GLN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 96 GLN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.071 38672 Z= 0.457 Angle : 0.837 6.893 52432 Z= 0.455 Chirality : 0.055 0.234 5584 Planarity : 0.008 0.078 6880 Dihedral : 6.151 25.370 5360 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.12), residues: 4760 helix: 1.18 (0.12), residues: 1872 sheet: 0.04 (0.19), residues: 712 loop : -0.05 (0.14), residues: 2176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 639 time to evaluate : 4.505 Fit side-chains outliers start: 61 outliers final: 27 residues processed: 676 average time/residue: 1.7375 time to fit residues: 1408.7443 Evaluate side-chains 664 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 637 time to evaluate : 4.586 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 26 residues processed: 1 average time/residue: 1.9086 time to fit residues: 8.5374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 153 optimal weight: 10.0000 chunk 410 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 267 optimal weight: 0.0980 chunk 112 optimal weight: 2.9990 chunk 456 optimal weight: 20.0000 chunk 379 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 151 optimal weight: 7.9990 chunk 239 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 96 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 96 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN F 36 ASN G 96 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN ** G 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN I 96 GLN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 96 GLN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 96 GLN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 38672 Z= 0.223 Angle : 0.634 6.049 52432 Z= 0.342 Chirality : 0.046 0.184 5584 Planarity : 0.005 0.047 6880 Dihedral : 5.642 23.241 5360 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.12), residues: 4760 helix: 1.55 (0.12), residues: 1872 sheet: 0.14 (0.19), residues: 696 loop : 0.16 (0.14), residues: 2192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 669 time to evaluate : 4.474 Fit side-chains outliers start: 51 outliers final: 32 residues processed: 700 average time/residue: 1.7039 time to fit residues: 1425.7115 Evaluate side-chains 690 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 658 time to evaluate : 4.746 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 30 residues processed: 2 average time/residue: 2.0550 time to fit residues: 11.3203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 440 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 260 optimal weight: 20.0000 chunk 333 optimal weight: 6.9990 chunk 258 optimal weight: 9.9990 chunk 384 optimal weight: 0.9990 chunk 255 optimal weight: 9.9990 chunk 454 optimal weight: 0.9980 chunk 284 optimal weight: 9.9990 chunk 277 optimal weight: 7.9990 chunk 210 optimal weight: 0.6980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 96 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 96 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** E 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 96 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN ** G 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN I 96 GLN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 96 GLN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 96 GLN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN ** O 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 38672 Z= 0.238 Angle : 0.646 6.311 52432 Z= 0.348 Chirality : 0.046 0.189 5584 Planarity : 0.005 0.049 6880 Dihedral : 5.594 23.288 5360 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.12), residues: 4760 helix: 1.44 (0.12), residues: 1920 sheet: 0.15 (0.19), residues: 696 loop : 0.23 (0.14), residues: 2144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 664 time to evaluate : 4.526 Fit side-chains outliers start: 45 outliers final: 29 residues processed: 695 average time/residue: 1.7578 time to fit residues: 1465.5093 Evaluate side-chains 688 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 659 time to evaluate : 4.436 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 29 residues processed: 0 time to fit residues: 6.2378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 281 optimal weight: 20.0000 chunk 181 optimal weight: 2.9990 chunk 271 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 289 optimal weight: 10.0000 chunk 309 optimal weight: 1.9990 chunk 224 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 357 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 96 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 96 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** E 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 96 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN ** G 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN I 96 GLN I 156 GLN ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 96 GLN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 96 GLN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 38672 Z= 0.160 Angle : 0.561 6.067 52432 Z= 0.300 Chirality : 0.043 0.173 5584 Planarity : 0.004 0.045 6880 Dihedral : 5.221 21.023 5360 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.12), residues: 4760 helix: 1.80 (0.12), residues: 1872 sheet: 0.17 (0.18), residues: 696 loop : 0.37 (0.14), residues: 2192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 662 time to evaluate : 4.689 Fit side-chains outliers start: 42 outliers final: 31 residues processed: 696 average time/residue: 1.7578 time to fit residues: 1469.1222 Evaluate side-chains 691 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 660 time to evaluate : 4.272 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 31 residues processed: 0 time to fit residues: 6.3463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 413 optimal weight: 10.0000 chunk 435 optimal weight: 20.0000 chunk 397 optimal weight: 0.5980 chunk 423 optimal weight: 5.9990 chunk 255 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 332 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 383 optimal weight: 0.9990 chunk 400 optimal weight: 9.9990 chunk 422 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 96 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 45 GLN E 96 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** E 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 96 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN ** G 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN I 96 GLN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN ** I 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN ** K 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 96 GLN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN ** M 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 96 GLN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN ** O 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 38672 Z= 0.257 Angle : 0.657 6.378 52432 Z= 0.353 Chirality : 0.047 0.191 5584 Planarity : 0.005 0.057 6880 Dihedral : 5.526 22.852 5360 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.12), residues: 4760 helix: 1.52 (0.12), residues: 1920 sheet: 0.18 (0.18), residues: 696 loop : 0.31 (0.14), residues: 2144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 663 time to evaluate : 4.454 Fit side-chains outliers start: 48 outliers final: 35 residues processed: 698 average time/residue: 1.4664 time to fit residues: 1221.3591 Evaluate side-chains 691 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 656 time to evaluate : 2.849 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 33 residues processed: 2 average time/residue: 1.4080 time to fit residues: 7.2002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 278 optimal weight: 0.9980 chunk 448 optimal weight: 4.9990 chunk 273 optimal weight: 9.9990 chunk 212 optimal weight: 2.9990 chunk 311 optimal weight: 2.9990 chunk 470 optimal weight: 0.7980 chunk 432 optimal weight: 10.0000 chunk 374 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 289 optimal weight: 9.9990 chunk 229 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 96 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 96 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** E 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 96 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN ** G 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN I 96 GLN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN L 36 ASN M 96 GLN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 96 GLN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN ** O 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 38672 Z= 0.209 Angle : 0.616 6.420 52432 Z= 0.330 Chirality : 0.045 0.183 5584 Planarity : 0.005 0.056 6880 Dihedral : 5.412 22.166 5360 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.12), residues: 4760 helix: 1.72 (0.12), residues: 1872 sheet: 0.19 (0.18), residues: 696 loop : 0.33 (0.14), residues: 2192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 657 time to evaluate : 4.869 Fit side-chains outliers start: 44 outliers final: 34 residues processed: 692 average time/residue: 1.5264 time to fit residues: 1261.0361 Evaluate side-chains 688 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 654 time to evaluate : 3.199 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 34 residues processed: 0 time to fit residues: 4.4175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 297 optimal weight: 3.9990 chunk 398 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 345 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 375 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 385 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: