Starting phenix.real_space_refine on Sun Feb 18 02:25:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgn_21198/02_2024/6vgn_21198_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgn_21198/02_2024/6vgn_21198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgn_21198/02_2024/6vgn_21198.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgn_21198/02_2024/6vgn_21198.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgn_21198/02_2024/6vgn_21198_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgn_21198/02_2024/6vgn_21198_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.360 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: 5 Type Number sf(0) Gaussians S 119 5.16 5 C 12922 2.51 5 N 3444 2.21 5 O 3948 1.98 5 F 14 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20447 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1508 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "B" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1508 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "C" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1508 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "D" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1508 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "E" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1508 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "F" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1508 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "G" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1508 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "H" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "I" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "J" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "K" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "L" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "M" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "N" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "V" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Unusual residues: {'R0M': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="R0M V 1 " pdbres="WFP V 2 " Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'MP8:plan-1': 1, 'WFP:plan-2': 1, 'YCP:plan-1': 1, 'ALO:plan-1': 1, 'R0M:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "W" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Unusual residues: {'R0M': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="R0M W 1 " pdbres="WFP W 2 " Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'MP8:plan-1': 1, 'WFP:plan-2': 1, 'YCP:plan-1': 1, 'ALO:plan-1': 1, 'R0M:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "X" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Unusual residues: {'R0M': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="R0M X 1 " pdbres="WFP X 2 " Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'MP8:plan-1': 1, 'WFP:plan-2': 1, 'YCP:plan-1': 1, 'ALO:plan-1': 1, 'R0M:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Unusual residues: {'R0M': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="R0M Y 1 " pdbres="WFP Y 2 " Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'MP8:plan-1': 1, 'WFP:plan-2': 1, 'YCP:plan-1': 1, 'ALO:plan-1': 1, 'R0M:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "Z" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Unusual residues: {'R0M': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="R0M Z 1 " pdbres="WFP Z 2 " Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'MP8:plan-1': 1, 'WFP:plan-2': 1, 'YCP:plan-1': 1, 'ALO:plan-1': 1, 'R0M:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "a" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Unusual residues: {'R0M': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="R0M a 1 " pdbres="WFP a 2 " Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'MP8:plan-1': 1, 'WFP:plan-2': 1, 'YCP:plan-1': 1, 'ALO:plan-1': 1, 'R0M:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "b" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Unusual residues: {'R0M': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="R0M b 1 " pdbres="WFP b 2 " Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'MP8:plan-1': 1, 'WFP:plan-2': 1, 'YCP:plan-1': 1, 'ALO:plan-1': 1, 'R0M:plan-1': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 11.08, per 1000 atoms: 0.54 Number of scatterers: 20447 At special positions: 0 Unit cell: (115.54, 115.54, 117.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 119 16.00 F 14 9.00 O 3948 8.00 N 3444 7.00 C 12922 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=14, symmetry=0 Number of additional bonds: simple=14, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.72 Conformation dependent library (CDL) restraints added in 3.2 seconds 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4956 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 35 sheets defined 45.8% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.86 Creating SS restraints... Processing helix chain 'A' and resid 34 through 38 Processing helix chain 'A' and resid 50 through 66 removed outlier: 3.938A pdb=" N ASP A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 110 through 117 removed outlier: 3.564A pdb=" N LEU A 116 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 172 removed outlier: 4.283A pdb=" N ALA A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 removed outlier: 3.780A pdb=" N ARG A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 196 removed outlier: 3.722A pdb=" N LYS A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 38 Processing helix chain 'B' and resid 50 through 66 removed outlier: 3.938A pdb=" N ASP B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 95 Processing helix chain 'B' and resid 110 through 117 removed outlier: 3.563A pdb=" N LEU B 116 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 172 removed outlier: 4.284A pdb=" N ALA B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 185 removed outlier: 3.780A pdb=" N ARG B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 196 removed outlier: 3.722A pdb=" N LYS B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 38 Processing helix chain 'C' and resid 50 through 66 removed outlier: 3.938A pdb=" N ASP C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 95 Processing helix chain 'C' and resid 110 through 117 removed outlier: 3.563A pdb=" N LEU C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 172 removed outlier: 4.283A pdb=" N ALA C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 removed outlier: 3.780A pdb=" N ARG C 185 " --> pdb=" O LYS C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 removed outlier: 3.722A pdb=" N LYS C 195 " --> pdb=" O ALA C 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 38 Processing helix chain 'D' and resid 50 through 66 removed outlier: 3.938A pdb=" N ASP D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 95 Processing helix chain 'D' and resid 110 through 117 removed outlier: 3.564A pdb=" N LEU D 116 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 172 removed outlier: 4.283A pdb=" N ALA D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 185 removed outlier: 3.780A pdb=" N ARG D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 196 removed outlier: 3.722A pdb=" N LYS D 195 " --> pdb=" O ALA D 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 38 Processing helix chain 'E' and resid 50 through 66 removed outlier: 3.938A pdb=" N ASP E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 95 Processing helix chain 'E' and resid 110 through 117 removed outlier: 3.562A pdb=" N LEU E 116 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 172 removed outlier: 4.283A pdb=" N ALA E 154 " --> pdb=" O LEU E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 185 removed outlier: 3.780A pdb=" N ARG E 185 " --> pdb=" O LYS E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 196 removed outlier: 3.722A pdb=" N LYS E 195 " --> pdb=" O ALA E 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 38 Processing helix chain 'F' and resid 50 through 66 removed outlier: 3.937A pdb=" N ASP F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 95 Processing helix chain 'F' and resid 110 through 117 removed outlier: 3.563A pdb=" N LEU F 116 " --> pdb=" O ALA F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 172 removed outlier: 4.283A pdb=" N ALA F 154 " --> pdb=" O LEU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 185 removed outlier: 3.779A pdb=" N ARG F 185 " --> pdb=" O LYS F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 removed outlier: 3.721A pdb=" N LYS F 195 " --> pdb=" O ALA F 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 38 Processing helix chain 'G' and resid 50 through 66 removed outlier: 3.938A pdb=" N ASP G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 95 Processing helix chain 'G' and resid 110 through 117 removed outlier: 3.563A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 172 removed outlier: 4.283A pdb=" N ALA G 154 " --> pdb=" O LEU G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 185 removed outlier: 3.780A pdb=" N ARG G 185 " --> pdb=" O LYS G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 196 removed outlier: 3.721A pdb=" N LYS G 195 " --> pdb=" O ALA G 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 27 removed outlier: 3.626A pdb=" N GLU H 27 " --> pdb=" O ARG H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 54 Processing helix chain 'H' and resid 71 through 83 Processing helix chain 'H' and resid 98 through 105 removed outlier: 3.593A pdb=" N LEU H 103 " --> pdb=" O GLY H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 158 removed outlier: 3.900A pdb=" N ILE H 138 " --> pdb=" O ALA H 134 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU H 141 " --> pdb=" O ALA H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 169 Processing helix chain 'H' and resid 177 through 183 Processing helix chain 'I' and resid 16 through 27 removed outlier: 3.625A pdb=" N GLU I 27 " --> pdb=" O ARG I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 54 Processing helix chain 'I' and resid 71 through 83 Processing helix chain 'I' and resid 98 through 105 removed outlier: 3.593A pdb=" N LEU I 103 " --> pdb=" O GLY I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 158 removed outlier: 3.900A pdb=" N ILE I 138 " --> pdb=" O ALA I 134 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU I 141 " --> pdb=" O ALA I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 169 Processing helix chain 'I' and resid 177 through 183 Processing helix chain 'J' and resid 16 through 27 removed outlier: 3.626A pdb=" N GLU J 27 " --> pdb=" O ARG J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 54 Processing helix chain 'J' and resid 71 through 83 Processing helix chain 'J' and resid 98 through 105 removed outlier: 3.592A pdb=" N LEU J 103 " --> pdb=" O GLY J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 158 removed outlier: 3.899A pdb=" N ILE J 138 " --> pdb=" O ALA J 134 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU J 141 " --> pdb=" O ALA J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 169 Processing helix chain 'J' and resid 177 through 183 Processing helix chain 'K' and resid 16 through 27 removed outlier: 3.625A pdb=" N GLU K 27 " --> pdb=" O ARG K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 54 Processing helix chain 'K' and resid 71 through 83 Processing helix chain 'K' and resid 98 through 105 removed outlier: 3.592A pdb=" N LEU K 103 " --> pdb=" O GLY K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 158 removed outlier: 3.900A pdb=" N ILE K 138 " --> pdb=" O ALA K 134 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU K 141 " --> pdb=" O ALA K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 162 through 169 Processing helix chain 'K' and resid 177 through 183 Processing helix chain 'L' and resid 16 through 27 removed outlier: 3.626A pdb=" N GLU L 27 " --> pdb=" O ARG L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 54 Processing helix chain 'L' and resid 71 through 83 Processing helix chain 'L' and resid 98 through 105 removed outlier: 3.592A pdb=" N LEU L 103 " --> pdb=" O GLY L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 158 removed outlier: 3.900A pdb=" N ILE L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU L 141 " --> pdb=" O ALA L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 169 Processing helix chain 'L' and resid 177 through 183 Processing helix chain 'M' and resid 16 through 27 removed outlier: 3.626A pdb=" N GLU M 27 " --> pdb=" O ARG M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 54 Processing helix chain 'M' and resid 71 through 83 Processing helix chain 'M' and resid 98 through 105 removed outlier: 3.592A pdb=" N LEU M 103 " --> pdb=" O GLY M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 158 removed outlier: 3.900A pdb=" N ILE M 138 " --> pdb=" O ALA M 134 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU M 141 " --> pdb=" O ALA M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 169 Processing helix chain 'M' and resid 177 through 183 Processing helix chain 'N' and resid 16 through 27 removed outlier: 3.626A pdb=" N GLU N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 54 Processing helix chain 'N' and resid 71 through 83 Processing helix chain 'N' and resid 98 through 105 removed outlier: 3.592A pdb=" N LEU N 103 " --> pdb=" O GLY N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 133 through 158 removed outlier: 3.900A pdb=" N ILE N 138 " --> pdb=" O ALA N 134 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU N 141 " --> pdb=" O ALA N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 169 Processing helix chain 'N' and resid 177 through 183 Processing sheet with id= A, first strand: chain 'A' and resid 18 through 23 Processing sheet with id= B, first strand: chain 'A' and resid 41 through 44 removed outlier: 6.473A pdb=" N THR A 73 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU A 44 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR A 75 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A 202 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 107 through 109 removed outlier: 6.885A pdb=" N ARG A 131 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 18 through 23 Processing sheet with id= E, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.474A pdb=" N THR B 73 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU B 44 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR B 75 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR B 202 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 107 through 109 removed outlier: 6.885A pdb=" N ARG B 131 " --> pdb=" O ALA B 108 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 18 through 23 Processing sheet with id= H, first strand: chain 'C' and resid 41 through 44 removed outlier: 6.474A pdb=" N THR C 73 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU C 44 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N TYR C 75 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR C 202 " --> pdb=" O ALA C 126 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 107 through 109 removed outlier: 6.884A pdb=" N ARG C 131 " --> pdb=" O ALA C 108 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 18 through 23 Processing sheet with id= K, first strand: chain 'D' and resid 41 through 44 removed outlier: 6.474A pdb=" N THR D 73 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU D 44 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR D 75 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR D 202 " --> pdb=" O ALA D 126 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 107 through 109 removed outlier: 6.884A pdb=" N ARG D 131 " --> pdb=" O ALA D 108 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 18 through 23 Processing sheet with id= N, first strand: chain 'E' and resid 41 through 44 removed outlier: 6.473A pdb=" N THR E 73 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU E 44 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N TYR E 75 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR E 202 " --> pdb=" O ALA E 126 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 107 through 109 removed outlier: 6.885A pdb=" N ARG E 131 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 18 through 23 Processing sheet with id= Q, first strand: chain 'F' and resid 41 through 44 removed outlier: 6.473A pdb=" N THR F 73 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU F 44 " --> pdb=" O THR F 73 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR F 75 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR F 202 " --> pdb=" O ALA F 126 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 107 through 109 removed outlier: 6.885A pdb=" N ARG F 131 " --> pdb=" O ALA F 108 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 18 through 23 Processing sheet with id= T, first strand: chain 'G' and resid 41 through 44 removed outlier: 6.474A pdb=" N THR G 73 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU G 44 " --> pdb=" O THR G 73 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR G 75 " --> pdb=" O LEU G 44 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR G 202 " --> pdb=" O ALA G 126 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 107 through 109 removed outlier: 6.884A pdb=" N ARG G 131 " --> pdb=" O ALA G 108 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 29 through 32 removed outlier: 6.340A pdb=" N SER H 61 " --> pdb=" O ILE H 30 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU H 32 " --> pdb=" O SER H 61 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR H 63 " --> pdb=" O LEU H 32 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N HIS H 188 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 95 through 97 removed outlier: 6.635A pdb=" N ARG H 119 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N MET H 122 " --> pdb=" O ARG H 173 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ARG H 173 " --> pdb=" O MET H 122 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 29 through 32 removed outlier: 6.341A pdb=" N SER I 61 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU I 32 " --> pdb=" O SER I 61 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR I 63 " --> pdb=" O LEU I 32 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N HIS I 188 " --> pdb=" O ALA I 114 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 95 through 97 removed outlier: 6.635A pdb=" N ARG I 119 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET I 122 " --> pdb=" O ARG I 173 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ARG I 173 " --> pdb=" O MET I 122 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 29 through 32 removed outlier: 6.341A pdb=" N SER J 61 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU J 32 " --> pdb=" O SER J 61 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR J 63 " --> pdb=" O LEU J 32 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N HIS J 188 " --> pdb=" O ALA J 114 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 95 through 97 removed outlier: 6.635A pdb=" N ARG J 119 " --> pdb=" O ALA J 96 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET J 122 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG J 173 " --> pdb=" O MET J 122 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.341A pdb=" N SER K 61 " --> pdb=" O ILE K 30 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU K 32 " --> pdb=" O SER K 61 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR K 63 " --> pdb=" O LEU K 32 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N HIS K 188 " --> pdb=" O ALA K 114 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'K' and resid 95 through 97 removed outlier: 6.635A pdb=" N ARG K 119 " --> pdb=" O ALA K 96 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET K 122 " --> pdb=" O ARG K 173 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ARG K 173 " --> pdb=" O MET K 122 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'L' and resid 29 through 32 removed outlier: 6.342A pdb=" N SER L 61 " --> pdb=" O ILE L 30 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU L 32 " --> pdb=" O SER L 61 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR L 63 " --> pdb=" O LEU L 32 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N HIS L 188 " --> pdb=" O ALA L 114 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'L' and resid 95 through 97 removed outlier: 6.636A pdb=" N ARG L 119 " --> pdb=" O ALA L 96 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET L 122 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ARG L 173 " --> pdb=" O MET L 122 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.340A pdb=" N SER M 61 " --> pdb=" O ILE M 30 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU M 32 " --> pdb=" O SER M 61 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR M 63 " --> pdb=" O LEU M 32 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N HIS M 188 " --> pdb=" O ALA M 114 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'M' and resid 95 through 97 removed outlier: 6.635A pdb=" N ARG M 119 " --> pdb=" O ALA M 96 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N MET M 122 " --> pdb=" O ARG M 173 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG M 173 " --> pdb=" O MET M 122 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.341A pdb=" N SER N 61 " --> pdb=" O ILE N 30 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU N 32 " --> pdb=" O SER N 61 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR N 63 " --> pdb=" O LEU N 32 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N HIS N 188 " --> pdb=" O ALA N 114 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'N' and resid 95 through 97 removed outlier: 6.636A pdb=" N ARG N 119 " --> pdb=" O ALA N 96 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET N 122 " --> pdb=" O ARG N 173 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ARG N 173 " --> pdb=" O MET N 122 " (cutoff:3.500A) 945 hydrogen bonds defined for protein. 2646 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: 7.14 Time building geometry restraints manager: 9.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4123 1.31 - 1.44: 5408 1.44 - 1.57: 10971 1.57 - 1.70: 43 1.70 - 1.83: 217 Bond restraints: 20762 Sorted by residual: bond pdb=" N MP8 X 7 " pdb=" CA MP8 X 7 " ideal model delta sigma weight residual 1.466 1.312 0.154 1.50e-02 4.44e+03 1.06e+02 bond pdb=" N MP8 b 7 " pdb=" CA MP8 b 7 " ideal model delta sigma weight residual 1.466 1.312 0.154 1.50e-02 4.44e+03 1.05e+02 bond pdb=" N MP8 Z 7 " pdb=" CA MP8 Z 7 " ideal model delta sigma weight residual 1.466 1.312 0.154 1.50e-02 4.44e+03 1.05e+02 bond pdb=" N MP8 V 7 " pdb=" CA MP8 V 7 " ideal model delta sigma weight residual 1.466 1.312 0.154 1.50e-02 4.44e+03 1.05e+02 bond pdb=" N MP8 W 7 " pdb=" CA MP8 W 7 " ideal model delta sigma weight residual 1.466 1.312 0.154 1.50e-02 4.44e+03 1.05e+02 ... (remaining 20757 not shown) Histogram of bond angle deviations from ideal: 94.19 - 102.04: 126 102.04 - 109.90: 4837 109.90 - 117.75: 10577 117.75 - 125.61: 12298 125.61 - 133.46: 225 Bond angle restraints: 28063 Sorted by residual: angle pdb=" C MP8 a 7 " pdb=" CA MP8 a 7 " pdb=" CB MP8 a 7 " ideal model delta sigma weight residual 110.10 127.10 -17.00 1.90e+00 2.77e-01 8.01e+01 angle pdb=" C MP8 Y 7 " pdb=" CA MP8 Y 7 " pdb=" CB MP8 Y 7 " ideal model delta sigma weight residual 110.10 127.10 -17.00 1.90e+00 2.77e-01 8.00e+01 angle pdb=" C MP8 W 7 " pdb=" CA MP8 W 7 " pdb=" CB MP8 W 7 " ideal model delta sigma weight residual 110.10 127.07 -16.97 1.90e+00 2.77e-01 7.98e+01 angle pdb=" C MP8 V 7 " pdb=" CA MP8 V 7 " pdb=" CB MP8 V 7 " ideal model delta sigma weight residual 110.10 127.06 -16.96 1.90e+00 2.77e-01 7.97e+01 angle pdb=" C MP8 b 7 " pdb=" CA MP8 b 7 " pdb=" CB MP8 b 7 " ideal model delta sigma weight residual 110.10 127.06 -16.96 1.90e+00 2.77e-01 7.97e+01 ... (remaining 28058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.31: 12348 24.31 - 48.62: 217 48.62 - 72.93: 49 72.93 - 97.24: 35 97.24 - 121.56: 7 Dihedral angle restraints: 12656 sinusoidal: 4977 harmonic: 7679 Sorted by residual: dihedral pdb=" C MP8 b 7 " pdb=" N MP8 b 7 " pdb=" CA MP8 b 7 " pdb=" CB MP8 b 7 " ideal model delta harmonic sigma weight residual -122.60 -170.85 48.25 0 2.50e+00 1.60e-01 3.73e+02 dihedral pdb=" C MP8 W 7 " pdb=" N MP8 W 7 " pdb=" CA MP8 W 7 " pdb=" CB MP8 W 7 " ideal model delta harmonic sigma weight residual -122.60 -170.83 48.23 0 2.50e+00 1.60e-01 3.72e+02 dihedral pdb=" C MP8 X 7 " pdb=" N MP8 X 7 " pdb=" CA MP8 X 7 " pdb=" CB MP8 X 7 " ideal model delta harmonic sigma weight residual -122.60 -170.81 48.21 0 2.50e+00 1.60e-01 3.72e+02 ... (remaining 12653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.480: 3241 0.480 - 0.961: 0 0.961 - 1.441: 0 1.441 - 1.921: 0 1.921 - 2.402: 7 Chirality restraints: 3248 Sorted by residual: chirality pdb=" CA MP8 b 7 " pdb=" N MP8 b 7 " pdb=" C MP8 b 7 " pdb=" CB MP8 b 7 " both_signs ideal model delta sigma weight residual False 2.72 0.32 2.40 2.00e-01 2.50e+01 1.44e+02 chirality pdb=" CA MP8 W 7 " pdb=" N MP8 W 7 " pdb=" C MP8 W 7 " pdb=" CB MP8 W 7 " both_signs ideal model delta sigma weight residual False 2.72 0.32 2.40 2.00e-01 2.50e+01 1.44e+02 chirality pdb=" CA MP8 X 7 " pdb=" N MP8 X 7 " pdb=" C MP8 X 7 " pdb=" CB MP8 X 7 " both_signs ideal model delta sigma weight residual False 2.72 0.32 2.40 2.00e-01 2.50e+01 1.44e+02 ... (remaining 3245 not shown) Planarity restraints: 3640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 149 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C ASP E 149 " -0.056 2.00e-02 2.50e+03 pdb=" O ASP E 149 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU E 150 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 149 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C ASP C 149 " -0.056 2.00e-02 2.50e+03 pdb=" O ASP C 149 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU C 150 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 149 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C ASP B 149 " 0.056 2.00e-02 2.50e+03 pdb=" O ASP B 149 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU B 150 " -0.019 2.00e-02 2.50e+03 ... (remaining 3637 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 8710 2.90 - 3.40: 20783 3.40 - 3.90: 36248 3.90 - 4.40: 43300 4.40 - 4.90: 67957 Nonbonded interactions: 176998 Sorted by model distance: nonbonded pdb=" N PRO E 32 " pdb=" O PRO E 32 " model vdw 2.401 2.496 nonbonded pdb=" N PRO B 32 " pdb=" O PRO B 32 " model vdw 2.401 2.496 nonbonded pdb=" N PRO A 32 " pdb=" O PRO A 32 " model vdw 2.401 2.496 nonbonded pdb=" N PRO D 32 " pdb=" O PRO D 32 " model vdw 2.401 2.496 nonbonded pdb=" N PRO G 32 " pdb=" O PRO G 32 " model vdw 2.401 2.496 ... (remaining 176993 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.570 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 56.330 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.210 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 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 : 0.021 0.213 20762 Z= 1.369 Angle : 1.786 17.003 28063 Z= 1.172 Chirality : 0.141 2.402 3248 Planarity : 0.009 0.040 3640 Dihedral : 12.019 121.555 7700 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % 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: 0.02 (0.15), residues: 2590 helix: -0.38 (0.12), residues: 1358 sheet: 2.07 (0.31), residues: 231 loop : 0.36 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.004 TRP L 174 HIS 0.010 0.003 HIS I 123 PHE 0.022 0.004 PHE D 43 TYR 0.038 0.008 TYR N 183 ARG 0.007 0.001 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 2.408 Fit side-chains REVERT: A 21 GLU cc_start: 0.8015 (tt0) cc_final: 0.7114 (pt0) REVERT: A 164 MET cc_start: 0.6760 (ttm) cc_final: 0.6526 (ttt) REVERT: A 175 ASP cc_start: 0.7455 (t70) cc_final: 0.7217 (m-30) REVERT: B 21 GLU cc_start: 0.7723 (tt0) cc_final: 0.7047 (pt0) REVERT: B 25 PHE cc_start: 0.5660 (m-10) cc_final: 0.5371 (m-80) REVERT: B 135 HIS cc_start: 0.6670 (m-70) cc_final: 0.6443 (m170) REVERT: B 164 MET cc_start: 0.6960 (ttm) cc_final: 0.6564 (ttt) REVERT: B 175 ASP cc_start: 0.7556 (t70) cc_final: 0.7194 (m-30) REVERT: C 21 GLU cc_start: 0.7347 (tt0) cc_final: 0.7034 (pt0) REVERT: C 135 HIS cc_start: 0.6446 (m-70) cc_final: 0.6100 (m-70) REVERT: C 164 MET cc_start: 0.6904 (ttm) cc_final: 0.6570 (ttt) REVERT: C 175 ASP cc_start: 0.7664 (t70) cc_final: 0.6878 (m-30) REVERT: D 164 MET cc_start: 0.6615 (ttm) cc_final: 0.6242 (ttt) REVERT: D 190 THR cc_start: 0.8332 (p) cc_final: 0.7975 (t) REVERT: E 21 GLU cc_start: 0.7310 (tt0) cc_final: 0.6957 (pt0) REVERT: E 164 MET cc_start: 0.6483 (ttm) cc_final: 0.6117 (ttt) REVERT: F 21 GLU cc_start: 0.7898 (tt0) cc_final: 0.7157 (pt0) REVERT: F 95 TYR cc_start: 0.8138 (t80) cc_final: 0.7915 (t80) REVERT: F 164 MET cc_start: 0.6634 (ttm) cc_final: 0.6249 (ttt) REVERT: G 164 MET cc_start: 0.7029 (ttm) cc_final: 0.6675 (ttt) REVERT: G 175 ASP cc_start: 0.7464 (t70) cc_final: 0.6848 (m-30) REVERT: G 200 ILE cc_start: 0.8180 (mm) cc_final: 0.7971 (mt) REVERT: H 70 SER cc_start: 0.7951 (m) cc_final: 0.7720 (p) REVERT: H 150 MET cc_start: 0.7473 (ttt) cc_final: 0.7068 (ttt) REVERT: H 179 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8327 (mt-10) REVERT: I 70 SER cc_start: 0.8154 (m) cc_final: 0.7807 (p) REVERT: J 70 SER cc_start: 0.8173 (m) cc_final: 0.7889 (p) REVERT: J 166 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8261 (mt-10) REVERT: J 179 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8176 (mt-10) REVERT: K 75 MET cc_start: 0.8426 (mmt) cc_final: 0.8130 (tpp) REVERT: L 158 THR cc_start: 0.8268 (p) cc_final: 0.8054 (p) REVERT: L 163 GLU cc_start: 0.8364 (mp0) cc_final: 0.7685 (pm20) REVERT: M 79 ASP cc_start: 0.8229 (m-30) cc_final: 0.7992 (m-30) REVERT: M 163 GLU cc_start: 0.8287 (mp0) cc_final: 0.7809 (pm20) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.3283 time to fit residues: 226.6998 Evaluate side-chains 308 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 7.9990 chunk 191 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 197 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 228 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20762 Z= 0.219 Angle : 0.581 7.646 28063 Z= 0.304 Chirality : 0.041 0.134 3248 Planarity : 0.004 0.032 3640 Dihedral : 10.490 101.308 2975 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.61 % Allowed : 4.86 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % 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 (0.16), residues: 2590 helix: 1.07 (0.14), residues: 1351 sheet: 2.56 (0.27), residues: 294 loop : -0.31 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 174 HIS 0.005 0.001 HIS A 135 PHE 0.011 0.002 PHE K 175 TYR 0.013 0.002 TYR M 21 ARG 0.004 0.000 ARG F 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 392 time to evaluate : 2.421 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.6833 (ttm) cc_final: 0.6512 (ttt) REVERT: A 175 ASP cc_start: 0.7681 (t70) cc_final: 0.7323 (m-30) REVERT: B 164 MET cc_start: 0.7078 (ttm) cc_final: 0.6679 (ttt) REVERT: B 175 ASP cc_start: 0.7674 (t70) cc_final: 0.7371 (m-30) REVERT: C 21 GLU cc_start: 0.7548 (tt0) cc_final: 0.7107 (pt0) REVERT: C 164 MET cc_start: 0.6998 (ttm) cc_final: 0.6655 (ttt) REVERT: C 175 ASP cc_start: 0.7767 (t70) cc_final: 0.7113 (m-30) REVERT: D 164 MET cc_start: 0.6897 (ttm) cc_final: 0.6564 (ttt) REVERT: E 21 GLU cc_start: 0.7722 (tt0) cc_final: 0.7180 (pt0) REVERT: E 93 MET cc_start: 0.7973 (mtp) cc_final: 0.7756 (mtp) REVERT: E 164 MET cc_start: 0.6733 (ttm) cc_final: 0.6360 (ttt) REVERT: F 21 GLU cc_start: 0.7828 (tt0) cc_final: 0.7160 (pt0) REVERT: F 57 MET cc_start: 0.7328 (mtp) cc_final: 0.7126 (mtp) REVERT: F 93 MET cc_start: 0.7713 (mtp) cc_final: 0.7456 (mtp) REVERT: F 125 MET cc_start: 0.8754 (mtm) cc_final: 0.8363 (mtm) REVERT: F 164 MET cc_start: 0.6714 (ttm) cc_final: 0.6374 (ttt) REVERT: F 200 ILE cc_start: 0.8084 (mm) cc_final: 0.7879 (mt) REVERT: G 21 GLU cc_start: 0.7502 (tt0) cc_final: 0.6742 (pt0) REVERT: G 164 MET cc_start: 0.6845 (ttm) cc_final: 0.6501 (ttt) REVERT: G 175 ASP cc_start: 0.7684 (t70) cc_final: 0.7008 (m-30) REVERT: G 200 ILE cc_start: 0.8142 (mm) cc_final: 0.7897 (mt) REVERT: H 75 MET cc_start: 0.8327 (mmt) cc_final: 0.8099 (mmp) REVERT: H 150 MET cc_start: 0.7465 (ttt) cc_final: 0.7022 (ttt) REVERT: H 158 THR cc_start: 0.8422 (p) cc_final: 0.8197 (p) REVERT: H 183 TYR cc_start: 0.8245 (t80) cc_final: 0.7816 (t80) REVERT: I 22 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7476 (tm-30) REVERT: I 75 MET cc_start: 0.8012 (mmt) cc_final: 0.7710 (mmp) REVERT: I 109 LYS cc_start: 0.8305 (mttp) cc_final: 0.8061 (mmtm) REVERT: I 183 TYR cc_start: 0.8087 (t80) cc_final: 0.7871 (t80) REVERT: K 150 MET cc_start: 0.7383 (ttt) cc_final: 0.7103 (ttt) REVERT: K 163 GLU cc_start: 0.8287 (mp0) cc_final: 0.7902 (pm20) REVERT: K 182 GLU cc_start: 0.8445 (tp30) cc_final: 0.8130 (tp30) REVERT: L 163 GLU cc_start: 0.8479 (mp0) cc_final: 0.7824 (pm20) REVERT: M 109 LYS cc_start: 0.8055 (mttp) cc_final: 0.7838 (mmtm) REVERT: M 163 GLU cc_start: 0.8413 (mp0) cc_final: 0.7906 (pm20) outliers start: 13 outliers final: 8 residues processed: 400 average time/residue: 0.3457 time to fit residues: 205.2577 Evaluate side-chains 337 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 329 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain N residue 70 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 190 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 229 optimal weight: 6.9990 chunk 247 optimal weight: 8.9990 chunk 204 optimal weight: 7.9990 chunk 227 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 20762 Z= 0.446 Angle : 0.687 8.537 28063 Z= 0.353 Chirality : 0.046 0.184 3248 Planarity : 0.005 0.036 3640 Dihedral : 9.872 104.646 2975 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.23 % Allowed : 7.26 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 0.66 (0.16), residues: 2590 helix: 0.87 (0.14), residues: 1344 sheet: 2.17 (0.28), residues: 266 loop : -0.60 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 174 HIS 0.007 0.001 HIS G 135 PHE 0.021 0.002 PHE J 102 TYR 0.019 0.003 TYR D 206 ARG 0.005 0.001 ARG F 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 370 time to evaluate : 2.182 Fit side-chains REVERT: A 95 TYR cc_start: 0.8090 (t80) cc_final: 0.7695 (t80) REVERT: A 131 ARG cc_start: 0.7819 (ttp-170) cc_final: 0.7506 (ttt180) REVERT: A 175 ASP cc_start: 0.7865 (t70) cc_final: 0.7478 (m-30) REVERT: B 96 VAL cc_start: 0.7446 (t) cc_final: 0.7216 (m) REVERT: B 164 MET cc_start: 0.7201 (ttm) cc_final: 0.6823 (ttt) REVERT: B 175 ASP cc_start: 0.7771 (t70) cc_final: 0.7347 (m-30) REVERT: C 164 MET cc_start: 0.7116 (ttm) cc_final: 0.6800 (ttt) REVERT: C 170 ARG cc_start: 0.8311 (ttp-110) cc_final: 0.8105 (ttm-80) REVERT: C 175 ASP cc_start: 0.7744 (t70) cc_final: 0.7223 (m-30) REVERT: D 164 MET cc_start: 0.6995 (ttm) cc_final: 0.6656 (ttt) REVERT: D 175 ASP cc_start: 0.7716 (t70) cc_final: 0.7272 (m-30) REVERT: E 125 MET cc_start: 0.8701 (mtm) cc_final: 0.8411 (mtm) REVERT: E 164 MET cc_start: 0.6884 (ttm) cc_final: 0.6599 (ttt) REVERT: E 175 ASP cc_start: 0.7788 (t70) cc_final: 0.7201 (m-30) REVERT: F 125 MET cc_start: 0.8769 (mtm) cc_final: 0.8519 (mtm) REVERT: F 161 ARG cc_start: 0.7355 (mtp180) cc_final: 0.7100 (mtp-110) REVERT: F 164 MET cc_start: 0.7078 (ttm) cc_final: 0.6761 (ttt) REVERT: F 175 ASP cc_start: 0.7742 (t70) cc_final: 0.7258 (m-30) REVERT: G 164 MET cc_start: 0.7074 (ttm) cc_final: 0.6740 (ttt) REVERT: G 175 ASP cc_start: 0.7979 (t70) cc_final: 0.7241 (m-30) REVERT: H 150 MET cc_start: 0.7459 (ttt) cc_final: 0.7058 (ttt) REVERT: H 182 GLU cc_start: 0.8608 (tp30) cc_final: 0.8261 (tp30) REVERT: H 183 TYR cc_start: 0.8642 (t80) cc_final: 0.8330 (t80) REVERT: I 75 MET cc_start: 0.8016 (mmt) cc_final: 0.7814 (mmp) REVERT: I 109 LYS cc_start: 0.8452 (mttp) cc_final: 0.7922 (mmtm) REVERT: I 141 GLU cc_start: 0.7261 (tp30) cc_final: 0.7048 (tp30) REVERT: I 183 TYR cc_start: 0.8526 (t80) cc_final: 0.8281 (t80) REVERT: J 166 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8126 (mt-10) REVERT: K 109 LYS cc_start: 0.8583 (mttp) cc_final: 0.7954 (mmtm) REVERT: K 141 GLU cc_start: 0.7211 (tp30) cc_final: 0.6989 (tp30) REVERT: K 150 MET cc_start: 0.7465 (ttt) cc_final: 0.7217 (ttt) REVERT: K 182 GLU cc_start: 0.8635 (tp30) cc_final: 0.8169 (tp30) REVERT: L 109 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8062 (mmtm) REVERT: M 163 GLU cc_start: 0.8339 (mp0) cc_final: 0.7975 (pm20) outliers start: 26 outliers final: 13 residues processed: 390 average time/residue: 0.3907 time to fit residues: 218.6813 Evaluate side-chains 323 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 309 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 109 LYS Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain N residue 70 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 20762 Z= 0.169 Angle : 0.497 5.750 28063 Z= 0.259 Chirality : 0.040 0.157 3248 Planarity : 0.004 0.045 3640 Dihedral : 9.018 107.284 2975 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.78 % Favored : 97.07 % Rotamer: Outliers : 1.56 % Allowed : 8.49 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % 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: 1.03 (0.16), residues: 2590 helix: 1.30 (0.14), residues: 1358 sheet: 1.95 (0.28), residues: 266 loop : -0.52 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 174 HIS 0.005 0.001 HIS G 135 PHE 0.009 0.001 PHE L 175 TYR 0.020 0.001 TYR F 197 ARG 0.009 0.000 ARG G 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 331 time to evaluate : 2.405 Fit side-chains REVERT: A 21 GLU cc_start: 0.7696 (tt0) cc_final: 0.7076 (mt-10) REVERT: A 175 ASP cc_start: 0.7826 (t70) cc_final: 0.7406 (m-30) REVERT: B 135 HIS cc_start: 0.6870 (m-70) cc_final: 0.6635 (m170) REVERT: B 164 MET cc_start: 0.7015 (ttm) cc_final: 0.6637 (ttt) REVERT: B 175 ASP cc_start: 0.7769 (t70) cc_final: 0.7332 (m-30) REVERT: C 161 ARG cc_start: 0.7292 (mtp180) cc_final: 0.7083 (mtp-110) REVERT: C 164 MET cc_start: 0.6936 (ttm) cc_final: 0.6618 (ttt) REVERT: C 170 ARG cc_start: 0.8222 (ttp-110) cc_final: 0.8000 (ttm-80) REVERT: C 175 ASP cc_start: 0.7833 (t70) cc_final: 0.7214 (m-30) REVERT: D 135 HIS cc_start: 0.7367 (t-170) cc_final: 0.7115 (t-170) REVERT: D 161 ARG cc_start: 0.7245 (mtp180) cc_final: 0.6970 (mtp-110) REVERT: D 164 MET cc_start: 0.6911 (ttm) cc_final: 0.6591 (ttt) REVERT: D 175 ASP cc_start: 0.7655 (t70) cc_final: 0.7192 (m-30) REVERT: E 21 GLU cc_start: 0.7762 (tt0) cc_final: 0.7124 (mt-10) REVERT: E 125 MET cc_start: 0.8654 (mtm) cc_final: 0.8376 (mtm) REVERT: E 135 HIS cc_start: 0.7427 (t-170) cc_final: 0.7178 (t-170) REVERT: E 164 MET cc_start: 0.6552 (ttm) cc_final: 0.6282 (ttt) REVERT: E 175 ASP cc_start: 0.7816 (t70) cc_final: 0.7209 (m-30) REVERT: F 125 MET cc_start: 0.8771 (mtm) cc_final: 0.8431 (mtm) REVERT: F 164 MET cc_start: 0.6971 (ttm) cc_final: 0.6702 (ttt) REVERT: F 175 ASP cc_start: 0.7736 (t70) cc_final: 0.7282 (m-30) REVERT: G 164 MET cc_start: 0.6945 (ttm) cc_final: 0.6574 (ttt) REVERT: G 175 ASP cc_start: 0.8065 (t70) cc_final: 0.7308 (m-30) REVERT: H 150 MET cc_start: 0.7586 (ttt) cc_final: 0.7242 (ttt) REVERT: H 183 TYR cc_start: 0.8563 (t80) cc_final: 0.8234 (t80) REVERT: I 173 ARG cc_start: 0.7172 (ttt180) cc_final: 0.6964 (ptm160) REVERT: I 183 TYR cc_start: 0.8416 (t80) cc_final: 0.8216 (t80) REVERT: J 109 LYS cc_start: 0.8496 (mttm) cc_final: 0.8136 (mmtm) REVERT: J 166 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8012 (mt-10) REVERT: K 109 LYS cc_start: 0.8600 (mttp) cc_final: 0.7984 (mmtm) REVERT: K 150 MET cc_start: 0.7433 (ttt) cc_final: 0.7149 (ttt) REVERT: M 163 GLU cc_start: 0.8365 (mp0) cc_final: 0.7978 (pm20) REVERT: M 183 TYR cc_start: 0.8587 (t80) cc_final: 0.8358 (t80) outliers start: 33 outliers final: 20 residues processed: 350 average time/residue: 0.3673 time to fit residues: 188.5543 Evaluate side-chains 332 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 312 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 190 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 0.0980 chunk 138 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 GLN ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 20762 Z= 0.485 Angle : 0.662 7.407 28063 Z= 0.340 Chirality : 0.046 0.176 3248 Planarity : 0.005 0.046 3640 Dihedral : 9.355 103.029 2975 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.17 % Favored : 94.79 % Rotamer: Outliers : 2.12 % Allowed : 8.86 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 1.10 % Twisted General : 0.27 % 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: 0.48 (0.16), residues: 2590 helix: 0.86 (0.14), residues: 1344 sheet: 1.73 (0.28), residues: 266 loop : -0.78 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP M 174 HIS 0.006 0.002 HIS H 123 PHE 0.016 0.002 PHE I 102 TYR 0.028 0.003 TYR N 183 ARG 0.009 0.001 ARG G 185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 309 time to evaluate : 2.130 Fit side-chains REVERT: A 125 MET cc_start: 0.8471 (ptp) cc_final: 0.8267 (mtm) REVERT: A 175 ASP cc_start: 0.7910 (t70) cc_final: 0.7486 (m-30) REVERT: B 96 VAL cc_start: 0.7461 (t) cc_final: 0.7195 (m) REVERT: B 164 MET cc_start: 0.7247 (ttm) cc_final: 0.6871 (ttt) REVERT: B 175 ASP cc_start: 0.7942 (t70) cc_final: 0.7366 (m-30) REVERT: C 135 HIS cc_start: 0.6786 (m170) cc_final: 0.6416 (m170) REVERT: C 164 MET cc_start: 0.6929 (ttm) cc_final: 0.6618 (ttt) REVERT: C 175 ASP cc_start: 0.7789 (t70) cc_final: 0.7285 (m-30) REVERT: D 135 HIS cc_start: 0.7630 (t-170) cc_final: 0.7381 (t-170) REVERT: D 161 ARG cc_start: 0.7496 (mtp180) cc_final: 0.7290 (mtp180) REVERT: D 164 MET cc_start: 0.7115 (ttm) cc_final: 0.6765 (ttt) REVERT: D 175 ASP cc_start: 0.7917 (t70) cc_final: 0.7435 (m-30) REVERT: E 125 MET cc_start: 0.8639 (mtm) cc_final: 0.8364 (mtm) REVERT: E 161 ARG cc_start: 0.7279 (mtp180) cc_final: 0.7077 (mtp180) REVERT: E 164 MET cc_start: 0.6918 (ttm) cc_final: 0.6701 (ttt) REVERT: E 175 ASP cc_start: 0.7896 (t70) cc_final: 0.7294 (m-30) REVERT: F 125 MET cc_start: 0.8795 (mtm) cc_final: 0.8379 (mtm) REVERT: F 164 MET cc_start: 0.7120 (ttm) cc_final: 0.6790 (ttt) REVERT: F 175 ASP cc_start: 0.7910 (t70) cc_final: 0.7470 (m-30) REVERT: G 164 MET cc_start: 0.7053 (ttm) cc_final: 0.6730 (ttt) REVERT: G 175 ASP cc_start: 0.8045 (t70) cc_final: 0.7325 (m-30) REVERT: G 205 GLU cc_start: 0.7965 (pm20) cc_final: 0.7738 (mt-10) REVERT: H 150 MET cc_start: 0.7550 (ttt) cc_final: 0.7192 (ttt) REVERT: H 183 TYR cc_start: 0.8784 (t80) cc_final: 0.8418 (t80) REVERT: I 75 MET cc_start: 0.7940 (tpp) cc_final: 0.7724 (tpp) REVERT: J 91 TYR cc_start: 0.8817 (m-80) cc_final: 0.8546 (m-80) REVERT: J 95 MET cc_start: 0.8193 (ttp) cc_final: 0.7982 (ttp) REVERT: K 109 LYS cc_start: 0.8617 (mttp) cc_final: 0.7940 (mmtm) REVERT: K 141 GLU cc_start: 0.7263 (tp30) cc_final: 0.7039 (tp30) REVERT: K 182 GLU cc_start: 0.8675 (tp30) cc_final: 0.8258 (tp30) REVERT: L 109 LYS cc_start: 0.8521 (mmtm) cc_final: 0.8092 (mmtm) REVERT: M 163 GLU cc_start: 0.8370 (mp0) cc_final: 0.8026 (pm20) outliers start: 45 outliers final: 30 residues processed: 336 average time/residue: 0.3532 time to fit residues: 179.1189 Evaluate side-chains 329 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 299 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 35 GLU Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 190 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 6.9990 chunk 219 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 243 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 GLN E 136 GLN ** F 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20762 Z= 0.151 Angle : 0.492 8.059 28063 Z= 0.253 Chirality : 0.040 0.157 3248 Planarity : 0.004 0.052 3640 Dihedral : 8.593 105.744 2975 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.79 % Allowed : 9.57 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % 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: 1.04 (0.16), residues: 2590 helix: 1.38 (0.14), residues: 1358 sheet: 1.61 (0.27), residues: 266 loop : -0.52 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 174 HIS 0.004 0.001 HIS G 135 PHE 0.008 0.001 PHE K 175 TYR 0.019 0.001 TYR N 183 ARG 0.010 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 301 time to evaluate : 2.165 Fit side-chains REVERT: A 21 GLU cc_start: 0.7673 (tt0) cc_final: 0.7036 (mt-10) REVERT: A 175 ASP cc_start: 0.7873 (t70) cc_final: 0.7474 (m-30) REVERT: B 135 HIS cc_start: 0.6985 (m-70) cc_final: 0.6781 (m170) REVERT: B 164 MET cc_start: 0.6923 (ttm) cc_final: 0.6572 (ttt) REVERT: B 175 ASP cc_start: 0.7854 (t70) cc_final: 0.7329 (m-30) REVERT: B 207 ARG cc_start: 0.5377 (ttm-80) cc_final: 0.5144 (ttm-80) REVERT: C 93 MET cc_start: 0.8042 (mtp) cc_final: 0.7793 (mtp) REVERT: C 135 HIS cc_start: 0.6792 (m170) cc_final: 0.6497 (m170) REVERT: C 175 ASP cc_start: 0.7880 (t70) cc_final: 0.7295 (m-30) REVERT: D 164 MET cc_start: 0.6875 (ttm) cc_final: 0.6564 (ttt) REVERT: D 175 ASP cc_start: 0.7776 (t70) cc_final: 0.7323 (m-30) REVERT: E 125 MET cc_start: 0.8612 (mtm) cc_final: 0.8397 (mtm) REVERT: E 164 MET cc_start: 0.6637 (ttm) cc_final: 0.6316 (ttt) REVERT: E 175 ASP cc_start: 0.7937 (t70) cc_final: 0.7385 (m-30) REVERT: F 125 MET cc_start: 0.8813 (mtm) cc_final: 0.8481 (mtm) REVERT: F 164 MET cc_start: 0.6930 (ttm) cc_final: 0.6669 (ttt) REVERT: F 175 ASP cc_start: 0.7830 (t70) cc_final: 0.7435 (m-30) REVERT: G 39 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7750 (mm-30) REVERT: G 164 MET cc_start: 0.6918 (ttm) cc_final: 0.6583 (ttt) REVERT: G 175 ASP cc_start: 0.8120 (t70) cc_final: 0.7398 (m-30) REVERT: G 205 GLU cc_start: 0.7938 (pm20) cc_final: 0.7361 (tp30) REVERT: H 150 MET cc_start: 0.7635 (ttt) cc_final: 0.7308 (ttt) REVERT: H 183 TYR cc_start: 0.8640 (t80) cc_final: 0.8260 (t80) REVERT: J 91 TYR cc_start: 0.8748 (m-80) cc_final: 0.8458 (m-80) REVERT: J 109 LYS cc_start: 0.8521 (mttm) cc_final: 0.8161 (mmtm) REVERT: J 166 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8064 (mt-10) REVERT: J 183 TYR cc_start: 0.8638 (t80) cc_final: 0.8327 (t80) REVERT: K 109 LYS cc_start: 0.8613 (mttp) cc_final: 0.7962 (mmtm) REVERT: M 79 ASP cc_start: 0.8154 (m-30) cc_final: 0.7903 (m-30) outliers start: 38 outliers final: 26 residues processed: 322 average time/residue: 0.3425 time to fit residues: 165.0150 Evaluate side-chains 312 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 286 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 138 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 178 optimal weight: 30.0000 chunk 137 optimal weight: 8.9990 chunk 205 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 242 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20762 Z= 0.262 Angle : 0.534 5.784 28063 Z= 0.274 Chirality : 0.042 0.163 3248 Planarity : 0.004 0.055 3640 Dihedral : 8.553 106.293 2975 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.70 % Allowed : 9.71 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % 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: 1.01 (0.16), residues: 2590 helix: 1.42 (0.14), residues: 1344 sheet: 1.59 (0.27), residues: 266 loop : -0.61 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 174 HIS 0.004 0.001 HIS D 135 PHE 0.011 0.001 PHE L 175 TYR 0.024 0.002 TYR I 183 ARG 0.012 0.000 ARG D 185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 298 time to evaluate : 2.119 Fit side-chains REVERT: A 21 GLU cc_start: 0.7685 (tt0) cc_final: 0.7042 (mt-10) REVERT: A 175 ASP cc_start: 0.7896 (t70) cc_final: 0.7467 (m-30) REVERT: A 205 GLU cc_start: 0.7695 (pm20) cc_final: 0.7181 (mp0) REVERT: B 96 VAL cc_start: 0.7403 (t) cc_final: 0.7118 (m) REVERT: B 164 MET cc_start: 0.7044 (ttm) cc_final: 0.6677 (ttt) REVERT: B 175 ASP cc_start: 0.7869 (t70) cc_final: 0.7311 (m-30) REVERT: C 135 HIS cc_start: 0.6821 (m170) cc_final: 0.6568 (m170) REVERT: C 175 ASP cc_start: 0.7815 (t70) cc_final: 0.7243 (m-30) REVERT: C 200 ILE cc_start: 0.8111 (mm) cc_final: 0.7830 (mt) REVERT: D 164 MET cc_start: 0.6908 (ttm) cc_final: 0.6576 (ttt) REVERT: D 175 ASP cc_start: 0.7797 (t70) cc_final: 0.7357 (m-30) REVERT: E 125 MET cc_start: 0.8624 (mtm) cc_final: 0.8407 (mtm) REVERT: E 164 MET cc_start: 0.6731 (ttm) cc_final: 0.6409 (ttt) REVERT: E 175 ASP cc_start: 0.7969 (t70) cc_final: 0.7390 (m-30) REVERT: E 205 GLU cc_start: 0.8062 (pm20) cc_final: 0.7456 (tp30) REVERT: F 125 MET cc_start: 0.8781 (mtm) cc_final: 0.8396 (mtm) REVERT: F 164 MET cc_start: 0.7008 (ttm) cc_final: 0.6713 (ttt) REVERT: F 175 ASP cc_start: 0.7886 (t70) cc_final: 0.7464 (m-30) REVERT: G 39 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7777 (mm-30) REVERT: G 164 MET cc_start: 0.7026 (ttm) cc_final: 0.6660 (ttt) REVERT: G 175 ASP cc_start: 0.8136 (t70) cc_final: 0.7406 (m-30) REVERT: H 150 MET cc_start: 0.7598 (ttt) cc_final: 0.7248 (ttt) REVERT: H 183 TYR cc_start: 0.8723 (t80) cc_final: 0.8322 (t80) REVERT: J 91 TYR cc_start: 0.8731 (m-80) cc_final: 0.8519 (m-80) REVERT: J 109 LYS cc_start: 0.8503 (mttm) cc_final: 0.8141 (mmtm) REVERT: J 171 ARG cc_start: 0.6513 (mtm-85) cc_final: 0.6162 (ttp-110) REVERT: K 109 LYS cc_start: 0.8585 (mttp) cc_final: 0.7932 (mmtm) REVERT: M 79 ASP cc_start: 0.8137 (m-30) cc_final: 0.7904 (m-30) outliers start: 36 outliers final: 29 residues processed: 320 average time/residue: 0.3684 time to fit residues: 177.7511 Evaluate side-chains 336 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 307 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 190 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 220 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN ** F 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 20762 Z= 0.534 Angle : 0.693 7.857 28063 Z= 0.354 Chirality : 0.047 0.165 3248 Planarity : 0.005 0.055 3640 Dihedral : 9.198 109.109 2975 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.03 % Allowed : 9.85 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 1.10 % Twisted General : 0.27 % 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: 0.31 (0.16), residues: 2590 helix: 0.77 (0.14), residues: 1344 sheet: 1.51 (0.27), residues: 266 loop : -0.90 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 174 HIS 0.006 0.001 HIS N 123 PHE 0.016 0.002 PHE L 102 TYR 0.033 0.003 TYR I 183 ARG 0.014 0.001 ARG G 185 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 316 time to evaluate : 2.111 Fit side-chains REVERT: A 175 ASP cc_start: 0.7942 (t70) cc_final: 0.7474 (m-30) REVERT: A 205 GLU cc_start: 0.7728 (pm20) cc_final: 0.7227 (mp0) REVERT: B 93 MET cc_start: 0.8340 (mtp) cc_final: 0.8026 (mtp) REVERT: B 96 VAL cc_start: 0.7465 (t) cc_final: 0.7207 (m) REVERT: B 164 MET cc_start: 0.7256 (ttm) cc_final: 0.6897 (ttt) REVERT: B 175 ASP cc_start: 0.7910 (t70) cc_final: 0.7279 (m-30) REVERT: C 135 HIS cc_start: 0.6983 (m170) cc_final: 0.6698 (m-70) REVERT: C 175 ASP cc_start: 0.7807 (t70) cc_final: 0.7327 (m-30) REVERT: C 200 ILE cc_start: 0.8235 (mm) cc_final: 0.8002 (mt) REVERT: D 161 ARG cc_start: 0.7576 (mtp180) cc_final: 0.7229 (mtp-110) REVERT: D 164 MET cc_start: 0.7123 (ttm) cc_final: 0.6795 (ttt) REVERT: D 175 ASP cc_start: 0.7966 (t70) cc_final: 0.7508 (m-30) REVERT: D 185 ARG cc_start: 0.7032 (mtm110) cc_final: 0.6416 (mtt90) REVERT: E 125 MET cc_start: 0.8606 (mtm) cc_final: 0.8382 (mtm) REVERT: E 161 ARG cc_start: 0.7359 (mtp180) cc_final: 0.7120 (mtp180) REVERT: E 164 MET cc_start: 0.6902 (ttm) cc_final: 0.6677 (ttt) REVERT: E 175 ASP cc_start: 0.7957 (t70) cc_final: 0.7360 (m-30) REVERT: E 205 GLU cc_start: 0.8221 (pm20) cc_final: 0.7707 (tm-30) REVERT: F 125 MET cc_start: 0.8789 (mtm) cc_final: 0.8372 (mtm) REVERT: F 164 MET cc_start: 0.7080 (ttm) cc_final: 0.6753 (ttt) REVERT: F 175 ASP cc_start: 0.7908 (t70) cc_final: 0.7503 (m-30) REVERT: F 205 GLU cc_start: 0.8141 (pm20) cc_final: 0.7681 (mt-10) REVERT: G 164 MET cc_start: 0.7016 (ttm) cc_final: 0.6682 (ttt) REVERT: G 175 ASP cc_start: 0.7943 (t70) cc_final: 0.7367 (m-30) REVERT: H 150 MET cc_start: 0.7536 (ttt) cc_final: 0.7150 (ttt) REVERT: H 183 TYR cc_start: 0.8827 (t80) cc_final: 0.8427 (t80) REVERT: J 54 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7811 (mt-10) REVERT: J 166 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8165 (mt-10) REVERT: J 171 ARG cc_start: 0.6697 (mtm-85) cc_final: 0.6255 (ttp-110) REVERT: J 183 TYR cc_start: 0.8848 (t80) cc_final: 0.8562 (t80) REVERT: K 109 LYS cc_start: 0.8591 (mttp) cc_final: 0.8007 (mmtm) REVERT: L 109 LYS cc_start: 0.8490 (mmtm) cc_final: 0.8080 (mmtm) REVERT: M 163 GLU cc_start: 0.8322 (mp0) cc_final: 0.8062 (pm20) REVERT: M 166 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8169 (mt-10) REVERT: N 22 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7695 (mm-30) outliers start: 43 outliers final: 31 residues processed: 341 average time/residue: 0.3716 time to fit residues: 187.6572 Evaluate side-chains 338 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 306 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain N residue 22 GLU Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 190 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 3.9990 chunk 212 optimal weight: 6.9990 chunk 226 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN B 136 GLN E 136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20762 Z= 0.213 Angle : 0.524 5.459 28063 Z= 0.271 Chirality : 0.041 0.144 3248 Planarity : 0.004 0.059 3640 Dihedral : 8.543 108.134 2975 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.56 % Allowed : 10.84 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.78 (0.16), residues: 2590 helix: 1.25 (0.14), residues: 1351 sheet: 1.40 (0.27), residues: 266 loop : -0.74 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 174 HIS 0.004 0.001 HIS F 135 PHE 0.009 0.001 PHE L 175 TYR 0.024 0.002 TYR I 183 ARG 0.014 0.000 ARG G 185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 303 time to evaluate : 2.338 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7876 (tt0) cc_final: 0.7087 (mt-10) REVERT: A 175 ASP cc_start: 0.7945 (t70) cc_final: 0.7509 (m-30) REVERT: A 205 GLU cc_start: 0.7683 (pm20) cc_final: 0.7212 (mp0) REVERT: B 96 VAL cc_start: 0.7419 (t) cc_final: 0.7154 (m) REVERT: B 164 MET cc_start: 0.7055 (ttm) cc_final: 0.6725 (ttt) REVERT: B 175 ASP cc_start: 0.7921 (t70) cc_final: 0.7363 (m-30) REVERT: C 135 HIS cc_start: 0.6844 (m170) cc_final: 0.6630 (m-70) REVERT: C 175 ASP cc_start: 0.7705 (t70) cc_final: 0.7233 (m-30) REVERT: D 161 ARG cc_start: 0.7412 (mtp180) cc_final: 0.6853 (mtm110) REVERT: D 164 MET cc_start: 0.6784 (ttm) cc_final: 0.6492 (ttt) REVERT: D 175 ASP cc_start: 0.7838 (t70) cc_final: 0.7423 (m-30) REVERT: E 125 MET cc_start: 0.8602 (mtm) cc_final: 0.8393 (mtm) REVERT: E 164 MET cc_start: 0.6689 (ttm) cc_final: 0.6363 (ttt) REVERT: E 175 ASP cc_start: 0.7984 (t70) cc_final: 0.7424 (m-30) REVERT: E 205 GLU cc_start: 0.8150 (pm20) cc_final: 0.7496 (tp30) REVERT: F 125 MET cc_start: 0.8802 (mtm) cc_final: 0.8449 (mtm) REVERT: F 164 MET cc_start: 0.6928 (ttm) cc_final: 0.6657 (ttt) REVERT: F 175 ASP cc_start: 0.7892 (t70) cc_final: 0.7508 (m-30) REVERT: G 39 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7762 (mm-30) REVERT: G 164 MET cc_start: 0.6963 (ttm) cc_final: 0.6622 (ttt) REVERT: G 175 ASP cc_start: 0.7929 (t70) cc_final: 0.7386 (m-30) REVERT: H 171 ARG cc_start: 0.6738 (mtm-85) cc_final: 0.6389 (ttp-110) REVERT: H 183 TYR cc_start: 0.8742 (t80) cc_final: 0.8390 (t80) REVERT: J 91 TYR cc_start: 0.8660 (m-80) cc_final: 0.8395 (m-80) REVERT: J 109 LYS cc_start: 0.8521 (mttm) cc_final: 0.8162 (mmtm) REVERT: J 171 ARG cc_start: 0.6346 (mtm-85) cc_final: 0.6057 (ttp-110) REVERT: J 183 TYR cc_start: 0.8798 (t80) cc_final: 0.8483 (t80) REVERT: K 109 LYS cc_start: 0.8567 (mttp) cc_final: 0.8005 (mmtm) REVERT: K 171 ARG cc_start: 0.6551 (mtm-85) cc_final: 0.6332 (mtm110) REVERT: M 79 ASP cc_start: 0.8190 (m-30) cc_final: 0.7930 (m-30) REVERT: N 171 ARG cc_start: 0.6475 (mtp180) cc_final: 0.6209 (mtm-85) outliers start: 33 outliers final: 31 residues processed: 322 average time/residue: 0.3471 time to fit residues: 167.5368 Evaluate side-chains 332 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 301 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 190 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 166 optimal weight: 4.9990 chunk 251 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 chunk 199 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 158 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 20762 Z= 0.381 Angle : 0.612 6.932 28063 Z= 0.313 Chirality : 0.044 0.181 3248 Planarity : 0.005 0.061 3640 Dihedral : 8.879 108.842 2975 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.70 % Allowed : 10.47 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 0.55 (0.16), residues: 2590 helix: 1.06 (0.14), residues: 1344 sheet: 1.35 (0.26), residues: 266 loop : -0.84 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 174 HIS 0.006 0.001 HIS F 135 PHE 0.012 0.002 PHE L 175 TYR 0.030 0.002 TYR I 183 ARG 0.015 0.001 ARG G 185 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 310 time to evaluate : 2.188 Fit side-chains REVERT: A 175 ASP cc_start: 0.7944 (t70) cc_final: 0.7527 (m-30) REVERT: A 205 GLU cc_start: 0.7683 (pm20) cc_final: 0.7189 (mp0) REVERT: B 96 VAL cc_start: 0.7457 (t) cc_final: 0.7192 (m) REVERT: B 164 MET cc_start: 0.7119 (ttm) cc_final: 0.6748 (ttt) REVERT: B 175 ASP cc_start: 0.7943 (t70) cc_final: 0.7356 (m-30) REVERT: C 135 HIS cc_start: 0.6902 (m170) cc_final: 0.6660 (m-70) REVERT: C 175 ASP cc_start: 0.7800 (t70) cc_final: 0.7320 (m-30) REVERT: C 200 ILE cc_start: 0.8189 (mm) cc_final: 0.7944 (mt) REVERT: D 161 ARG cc_start: 0.7536 (mtp180) cc_final: 0.7180 (mtp-110) REVERT: D 164 MET cc_start: 0.7075 (ttm) cc_final: 0.6735 (ttt) REVERT: D 175 ASP cc_start: 0.7864 (t70) cc_final: 0.7432 (m-30) REVERT: E 125 MET cc_start: 0.8605 (mtm) cc_final: 0.8380 (mtm) REVERT: E 164 MET cc_start: 0.6776 (ttm) cc_final: 0.6507 (ttt) REVERT: E 175 ASP cc_start: 0.7989 (t70) cc_final: 0.7408 (m-30) REVERT: E 205 GLU cc_start: 0.8169 (pm20) cc_final: 0.7618 (tm-30) REVERT: F 125 MET cc_start: 0.8769 (mtm) cc_final: 0.8372 (mtm) REVERT: F 164 MET cc_start: 0.7035 (ttm) cc_final: 0.6722 (ttt) REVERT: F 175 ASP cc_start: 0.7866 (t70) cc_final: 0.7433 (m-30) REVERT: F 205 GLU cc_start: 0.8111 (pm20) cc_final: 0.7677 (mt-10) REVERT: G 39 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7764 (mm-30) REVERT: G 164 MET cc_start: 0.7065 (ttm) cc_final: 0.6686 (ttt) REVERT: G 175 ASP cc_start: 0.7956 (t70) cc_final: 0.7389 (m-30) REVERT: H 179 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8453 (mt-10) REVERT: H 183 TYR cc_start: 0.8854 (t80) cc_final: 0.8514 (t80) REVERT: J 91 TYR cc_start: 0.8724 (m-80) cc_final: 0.8417 (m-80) REVERT: J 171 ARG cc_start: 0.6365 (mtm-85) cc_final: 0.6032 (ttp-110) REVERT: J 183 TYR cc_start: 0.8858 (t80) cc_final: 0.8596 (t80) REVERT: K 109 LYS cc_start: 0.8609 (mttp) cc_final: 0.8042 (mmtm) REVERT: K 171 ARG cc_start: 0.6676 (mtm-85) cc_final: 0.6449 (mtm110) outliers start: 36 outliers final: 34 residues processed: 331 average time/residue: 0.3681 time to fit residues: 181.5770 Evaluate side-chains 340 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 306 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 190 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 184 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 200 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 175 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 GLN D 136 GLN E 136 GLN H 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.144624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.121769 restraints weight = 24091.874| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.25 r_work: 0.3260 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20762 Z= 0.156 Angle : 0.500 5.208 28063 Z= 0.259 Chirality : 0.040 0.144 3248 Planarity : 0.004 0.062 3640 Dihedral : 8.297 107.816 2975 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.56 % Allowed : 10.80 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % 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: 1.07 (0.16), residues: 2590 helix: 1.52 (0.14), residues: 1344 sheet: 1.32 (0.26), residues: 266 loop : -0.57 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 174 HIS 0.003 0.001 HIS D 135 PHE 0.007 0.001 PHE M 175 TYR 0.023 0.001 TYR I 183 ARG 0.014 0.000 ARG G 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4251.84 seconds wall clock time: 77 minutes 49.44 seconds (4669.44 seconds total)