Starting phenix.real_space_refine on Mon Feb 19 23:35:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9b_23722/02_2024/7m9b_23722_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9b_23722/02_2024/7m9b_23722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9b_23722/02_2024/7m9b_23722.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9b_23722/02_2024/7m9b_23722.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9b_23722/02_2024/7m9b_23722_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9b_23722/02_2024/7m9b_23722_updated.pdb" } resolution = 3.8 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= 0.000 sd= 0.002 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 P 74 5.49 5 S 96 5.16 5 C 16294 2.51 5 N 4756 2.21 5 O 4919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 245": "OD1" <-> "OD2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 144": "OD1" <-> "OD2" Residue "E PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "F TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 270": "OE1" <-> "OE2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 245": "OD1" <-> "OD2" Residue "H TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 116": "NH1" <-> "NH2" Residue "J PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 139": "OE1" <-> "OE2" Residue "J PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 57": "NH1" <-> "NH2" Residue "K TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 183": "OD1" <-> "OD2" Residue "K PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26139 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "B" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "C" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "F" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2060 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 247} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "H" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2054 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 247} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "I" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "J" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2058 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 247} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2062 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 247} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "M" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 567 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "N" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 540 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.93, per 1000 atoms: 0.53 Number of scatterers: 26139 At special positions: 0 Unit cell: (144.97, 144.97, 171.57, 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 96 16.00 P 74 15.00 O 4919 8.00 N 4756 7.00 C 16294 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.87 Conformation dependent library (CDL) restraints added in 4.0 seconds 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5784 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 151 helices and 14 sheets defined 55.2% alpha, 7.0% beta 24 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 10.05 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 removed outlier: 3.504A pdb=" N LEU A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 52 Processing helix chain 'A' and resid 66 through 76 removed outlier: 3.537A pdb=" N ASP A 71 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 112 Processing helix chain 'A' and resid 122 through 135 removed outlier: 3.528A pdb=" N LYS A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.537A pdb=" N PHE A 154 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG A 158 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA A 161 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP A 163 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 182 Processing helix chain 'A' and resid 184 through 187 No H-bonds generated for 'chain 'A' and resid 184 through 187' Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.893A pdb=" N ILE A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 258 Processing helix chain 'A' and resid 265 through 273 removed outlier: 3.564A pdb=" N ALA A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS A 273 " --> pdb=" O GLN A 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 28 Processing helix chain 'B' and resid 37 through 52 Processing helix chain 'B' and resid 66 through 76 removed outlier: 3.569A pdb=" N TYR B 75 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 151 through 163 removed outlier: 3.534A pdb=" N ALA B 155 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 180 Processing helix chain 'B' and resid 184 through 187 No H-bonds generated for 'chain 'B' and resid 184 through 187' Processing helix chain 'B' and resid 201 through 214 removed outlier: 3.709A pdb=" N LYS B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 removed outlier: 4.779A pdb=" N ILE B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 257 Processing helix chain 'B' and resid 265 through 274 removed outlier: 4.250A pdb=" N GLN B 269 " --> pdb=" O LYS B 265 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU B 274 " --> pdb=" O GLU B 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 28 Processing helix chain 'C' and resid 37 through 52 Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 102 through 113 removed outlier: 3.616A pdb=" N LEU C 113 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 135 Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 151 through 163 removed outlier: 3.980A pdb=" N ALA C 155 " --> pdb=" O PRO C 151 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 182 removed outlier: 4.894A pdb=" N ARG C 182 " --> pdb=" O ALA C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 189 removed outlier: 3.848A pdb=" N GLU C 188 " --> pdb=" O GLU C 184 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 184 through 189' Processing helix chain 'C' and resid 201 through 214 Processing helix chain 'C' and resid 227 through 237 Processing helix chain 'C' and resid 241 through 258 removed outlier: 4.035A pdb=" N GLU C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 247 " --> pdb=" O ARG C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 274 Processing helix chain 'D' and resid 20 through 29 removed outlier: 3.615A pdb=" N GLU D 24 " --> pdb=" O TRP D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 52 Processing helix chain 'D' and resid 66 through 77 removed outlier: 3.517A pdb=" N HIS D 77 " --> pdb=" O TYR D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 112 Processing helix chain 'D' and resid 122 through 136 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 174 through 180 Processing helix chain 'D' and resid 184 through 189 Processing helix chain 'D' and resid 201 through 214 Processing helix chain 'D' and resid 227 through 237 removed outlier: 3.728A pdb=" N ARG D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA D 236 " --> pdb=" O ILE D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 257 Processing helix chain 'D' and resid 265 through 274 Processing helix chain 'E' and resid 20 through 28 Processing helix chain 'E' and resid 37 through 52 Processing helix chain 'E' and resid 66 through 76 Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 122 through 135 Processing helix chain 'E' and resid 146 through 148 No H-bonds generated for 'chain 'E' and resid 146 through 148' Processing helix chain 'E' and resid 152 through 163 removed outlier: 3.649A pdb=" N ALA E 155 " --> pdb=" O GLU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 182 removed outlier: 3.802A pdb=" N LYS E 181 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'E' and resid 201 through 214 Processing helix chain 'E' and resid 227 through 237 removed outlier: 4.453A pdb=" N ILE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 257 Processing helix chain 'E' and resid 265 through 274 Processing helix chain 'F' and resid 20 through 28 removed outlier: 3.933A pdb=" N LEU F 28 " --> pdb=" O GLU F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 52 removed outlier: 3.555A pdb=" N ASP F 44 " --> pdb=" O LYS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 76 Processing helix chain 'F' and resid 102 through 112 Processing helix chain 'F' and resid 122 through 135 removed outlier: 3.509A pdb=" N ASP F 127 " --> pdb=" O SER F 123 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR F 129 " --> pdb=" O PHE F 125 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE F 130 " --> pdb=" O ARG F 126 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY F 135 " --> pdb=" O GLU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 163 removed outlier: 3.865A pdb=" N ALA F 155 " --> pdb=" O PRO F 151 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP F 156 " --> pdb=" O GLU F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 181 Processing helix chain 'F' and resid 184 through 189 Processing helix chain 'F' and resid 202 through 214 Processing helix chain 'F' and resid 227 through 237 Processing helix chain 'F' and resid 241 through 258 removed outlier: 3.766A pdb=" N ARG F 258 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 274 Processing helix chain 'G' and resid 20 through 28 Processing helix chain 'G' and resid 37 through 52 Processing helix chain 'G' and resid 66 through 76 removed outlier: 3.551A pdb=" N ARG G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 112 Processing helix chain 'G' and resid 122 through 135 Processing helix chain 'G' and resid 154 through 163 Processing helix chain 'G' and resid 174 through 182 removed outlier: 3.956A pdb=" N ALA G 178 " --> pdb=" O ASP G 174 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL G 179 " --> pdb=" O ARG G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 189 Processing helix chain 'G' and resid 201 through 214 Processing helix chain 'G' and resid 227 through 237 removed outlier: 3.904A pdb=" N ARG G 231 " --> pdb=" O LYS G 227 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 257 Processing helix chain 'G' and resid 265 through 274 removed outlier: 3.907A pdb=" N GLN G 269 " --> pdb=" O LYS G 265 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU G 270 " --> pdb=" O ALA G 266 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL G 271 " --> pdb=" O VAL G 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA G 272 " --> pdb=" O LEU G 268 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS G 273 " --> pdb=" O GLN G 269 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU G 274 " --> pdb=" O GLU G 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 265 through 274' Processing helix chain 'H' and resid 20 through 29 removed outlier: 3.515A pdb=" N GLU H 24 " --> pdb=" O TRP H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 52 removed outlier: 3.822A pdb=" N GLY H 48 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS H 49 " --> pdb=" O TRP H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 76 removed outlier: 3.685A pdb=" N ARG H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 112 Processing helix chain 'H' and resid 122 through 135 Processing helix chain 'H' and resid 153 through 164 Processing helix chain 'H' and resid 174 through 182 removed outlier: 3.639A pdb=" N ILE H 180 " --> pdb=" O ASP H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 189 Processing helix chain 'H' and resid 201 through 214 Processing helix chain 'H' and resid 227 through 237 removed outlier: 3.755A pdb=" N ARG H 231 " --> pdb=" O LYS H 227 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE H 232 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 258 removed outlier: 4.187A pdb=" N LEU H 256 " --> pdb=" O ALA H 252 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER H 257 " --> pdb=" O ILE H 253 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG H 258 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 274 removed outlier: 3.553A pdb=" N VAL H 271 " --> pdb=" O VAL H 267 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA H 272 " --> pdb=" O LEU H 268 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS H 273 " --> pdb=" O GLN H 269 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 29 Processing helix chain 'I' and resid 37 through 52 Processing helix chain 'I' and resid 66 through 76 Processing helix chain 'I' and resid 104 through 112 Processing helix chain 'I' and resid 122 through 135 Processing helix chain 'I' and resid 146 through 148 No H-bonds generated for 'chain 'I' and resid 146 through 148' Processing helix chain 'I' and resid 151 through 163 removed outlier: 3.575A pdb=" N ALA I 155 " --> pdb=" O GLU I 152 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU I 162 " --> pdb=" O ASP I 159 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP I 163 " --> pdb=" O ILE I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 182 removed outlier: 4.033A pdb=" N ARG I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 189 Processing helix chain 'I' and resid 201 through 214 removed outlier: 3.656A pdb=" N GLN I 213 " --> pdb=" O GLU I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 237 removed outlier: 3.504A pdb=" N ILE I 232 " --> pdb=" O GLU I 228 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER I 235 " --> pdb=" O ARG I 231 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA I 236 " --> pdb=" O ILE I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 257 Processing helix chain 'I' and resid 265 through 274 Processing helix chain 'J' and resid 20 through 29 Processing helix chain 'J' and resid 37 through 52 Processing helix chain 'J' and resid 66 through 76 Processing helix chain 'J' and resid 102 through 113 removed outlier: 3.536A pdb=" N LEU J 113 " --> pdb=" O ILE J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 135 Processing helix chain 'J' and resid 146 through 148 No H-bonds generated for 'chain 'J' and resid 146 through 148' Processing helix chain 'J' and resid 151 through 163 removed outlier: 3.978A pdb=" N ALA J 155 " --> pdb=" O PRO J 151 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP J 156 " --> pdb=" O GLU J 152 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP J 159 " --> pdb=" O ALA J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 182 removed outlier: 4.291A pdb=" N ARG J 182 " --> pdb=" O ALA J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 189 Processing helix chain 'J' and resid 201 through 214 Processing helix chain 'J' and resid 227 through 237 removed outlier: 3.556A pdb=" N ILE J 232 " --> pdb=" O GLU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 257 Processing helix chain 'J' and resid 265 through 274 removed outlier: 3.653A pdb=" N ALA J 272 " --> pdb=" O LEU J 268 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS J 273 " --> pdb=" O GLN J 269 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU J 274 " --> pdb=" O GLU J 270 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 28 Processing helix chain 'K' and resid 37 through 52 Processing helix chain 'K' and resid 66 through 76 removed outlier: 3.709A pdb=" N ARG K 74 " --> pdb=" O CYS K 70 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 112 Processing helix chain 'K' and resid 122 through 135 Processing helix chain 'K' and resid 146 through 148 No H-bonds generated for 'chain 'K' and resid 146 through 148' Processing helix chain 'K' and resid 153 through 163 Processing helix chain 'K' and resid 174 through 182 removed outlier: 3.880A pdb=" N ARG K 182 " --> pdb=" O ALA K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 189 Processing helix chain 'K' and resid 201 through 215 Processing helix chain 'K' and resid 227 through 237 Processing helix chain 'K' and resid 241 through 257 removed outlier: 4.372A pdb=" N GLU K 246 " --> pdb=" O GLY K 242 " (cutoff:3.500A) Processing helix chain 'K' and resid 265 through 274 Processing helix chain 'L' and resid 20 through 29 Processing helix chain 'L' and resid 37 through 52 Processing helix chain 'L' and resid 66 through 76 removed outlier: 3.613A pdb=" N ARG L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 112 Processing helix chain 'L' and resid 122 through 135 Processing helix chain 'L' and resid 146 through 148 No H-bonds generated for 'chain 'L' and resid 146 through 148' Processing helix chain 'L' and resid 151 through 163 Processing helix chain 'L' and resid 174 through 182 removed outlier: 4.066A pdb=" N ASP L 177 " --> pdb=" O ASP L 174 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG L 182 " --> pdb=" O VAL L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 189 Processing helix chain 'L' and resid 202 through 214 Processing helix chain 'L' and resid 227 through 237 removed outlier: 4.377A pdb=" N ILE L 232 " --> pdb=" O GLU L 228 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU L 233 " --> pdb=" O MET L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 257 Processing helix chain 'L' and resid 265 through 274 removed outlier: 3.646A pdb=" N VAL L 271 " --> pdb=" O VAL L 267 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA L 272 " --> pdb=" O LEU L 268 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS L 273 " --> pdb=" O GLN L 269 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 193 through 195 removed outlier: 6.602A pdb=" N ARG A 57 " --> pdb=" O LEU A 194 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 193 through 195 removed outlier: 6.645A pdb=" N ARG B 57 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 193 through 196 removed outlier: 7.314A pdb=" N ARG C 57 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N PHE C 196 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C 59 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 170 " --> pdb=" O CYS C 56 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 193 through 195 removed outlier: 6.538A pdb=" N ARG D 57 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 170 " --> pdb=" O CYS D 56 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 193 through 195 removed outlier: 6.741A pdb=" N ARG E 57 " --> pdb=" O LEU E 194 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 169 through 172 removed outlier: 7.354A pdb=" N CYS F 56 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLY F 172 " --> pdb=" O CYS F 56 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N VAL F 58 " --> pdb=" O GLY F 172 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 91 through 95 removed outlier: 6.681A pdb=" N MET F 140 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE F 94 " --> pdb=" O MET F 140 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE F 142 " --> pdb=" O ILE F 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'G' and resid 193 through 195 removed outlier: 6.137A pdb=" N ARG G 57 " --> pdb=" O LEU G 194 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 193 through 195 removed outlier: 6.745A pdb=" N ARG H 57 " --> pdb=" O LEU H 194 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'I' and resid 193 through 196 removed outlier: 7.566A pdb=" N ARG I 57 " --> pdb=" O LEU I 194 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N PHE I 196 " --> pdb=" O ARG I 57 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL I 59 " --> pdb=" O PHE I 196 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'J' and resid 169 through 172 removed outlier: 6.985A pdb=" N CYS J 56 " --> pdb=" O LEU J 170 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N GLY J 172 " --> pdb=" O CYS J 56 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL J 58 " --> pdb=" O GLY J 172 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'J' and resid 91 through 95 removed outlier: 6.502A pdb=" N MET J 140 " --> pdb=" O VAL J 92 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ILE J 94 " --> pdb=" O MET J 140 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE J 142 " --> pdb=" O ILE J 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'K' and resid 193 through 195 removed outlier: 6.892A pdb=" N ARG K 57 " --> pdb=" O LEU K 194 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 193 through 195 removed outlier: 6.557A pdb=" N ARG L 57 " --> pdb=" O LEU L 194 " (cutoff:3.500A) 1134 hydrogen bonds defined for protein. 3240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 7.75 Time building geometry restraints manager: 11.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7514 1.34 - 1.45: 3809 1.45 - 1.57: 15061 1.57 - 1.69: 136 1.69 - 1.81: 144 Bond restraints: 26664 Sorted by residual: bond pdb=" N PRO K 90 " pdb=" CD PRO K 90 " ideal model delta sigma weight residual 1.473 1.554 -0.081 1.40e-02 5.10e+03 3.38e+01 bond pdb=" N LYS D 78 " pdb=" CA LYS D 78 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.41e-02 5.03e+03 4.37e+00 bond pdb=" CA LYS D 78 " pdb=" C LYS D 78 " ideal model delta sigma weight residual 1.524 1.549 -0.025 1.26e-02 6.30e+03 4.05e+00 bond pdb=" CB CYS H 56 " pdb=" SG CYS H 56 " ideal model delta sigma weight residual 1.808 1.762 0.046 3.30e-02 9.18e+02 1.94e+00 bond pdb=" CA ARG C 85 " pdb=" C ARG C 85 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.26e-02 6.30e+03 1.31e+00 ... (remaining 26659 not shown) Histogram of bond angle deviations from ideal: 92.03 - 101.00: 51 101.00 - 109.97: 3651 109.97 - 118.93: 18790 118.93 - 127.90: 13422 127.90 - 136.86: 215 Bond angle restraints: 36129 Sorted by residual: angle pdb=" N ASP C 174 " pdb=" CA ASP C 174 " pdb=" C ASP C 174 " ideal model delta sigma weight residual 114.75 98.33 16.42 1.26e+00 6.30e-01 1.70e+02 angle pdb=" N ARG C 85 " pdb=" CA ARG C 85 " pdb=" C ARG C 85 " ideal model delta sigma weight residual 109.81 136.86 -27.05 2.21e+00 2.05e-01 1.50e+02 angle pdb=" N THR C 173 " pdb=" CA THR C 173 " pdb=" C THR C 173 " ideal model delta sigma weight residual 110.56 132.84 -22.28 1.94e+00 2.66e-01 1.32e+02 angle pdb=" N LYS C 217 " pdb=" CA LYS C 217 " pdb=" C LYS C 217 " ideal model delta sigma weight residual 109.96 92.98 16.98 1.49e+00 4.50e-01 1.30e+02 angle pdb=" N ARG C 85 " pdb=" CA ARG C 85 " pdb=" CB ARG C 85 " ideal model delta sigma weight residual 110.37 92.03 18.34 1.78e+00 3.16e-01 1.06e+02 ... (remaining 36124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 15975 35.10 - 70.19: 432 70.19 - 105.29: 13 105.29 - 140.39: 8 140.39 - 175.48: 6 Dihedral angle restraints: 16434 sinusoidal: 7494 harmonic: 8940 Sorted by residual: dihedral pdb=" O2A ADP L 301 " pdb=" O3A ADP L 301 " pdb=" PA ADP L 301 " pdb=" PB ADP L 301 " ideal model delta sinusoidal sigma weight residual -60.00 115.49 -175.48 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP J 301 " pdb=" O3A ADP J 301 " pdb=" PA ADP J 301 " pdb=" PB ADP J 301 " ideal model delta sinusoidal sigma weight residual 300.00 128.31 171.69 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O1B ADP K 301 " pdb=" O3A ADP K 301 " pdb=" PB ADP K 301 " pdb=" PA ADP K 301 " ideal model delta sinusoidal sigma weight residual -60.00 101.87 -161.88 1 2.00e+01 2.50e-03 4.68e+01 ... (remaining 16431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 4056 0.159 - 0.318: 13 0.318 - 0.477: 1 0.477 - 0.636: 1 0.636 - 0.795: 1 Chirality restraints: 4072 Sorted by residual: chirality pdb=" CA THR C 173 " pdb=" N THR C 173 " pdb=" C THR C 173 " pdb=" CB THR C 173 " both_signs ideal model delta sigma weight residual False 2.53 1.73 0.80 2.00e-01 2.50e+01 1.58e+01 chirality pdb=" CA ARG C 85 " pdb=" N ARG C 85 " pdb=" C ARG C 85 " pdb=" CB ARG C 85 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.06e+00 chirality pdb=" CA GLN C 81 " pdb=" N GLN C 81 " pdb=" C GLN C 81 " pdb=" CB GLN C 81 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 4069 not shown) Planarity restraints: 4356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 85 " -0.044 5.00e-02 4.00e+02 6.58e-02 6.94e+00 pdb=" N PRO C 86 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 86 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 86 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 85 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO D 86 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 86 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 86 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 85 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO H 86 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO H 86 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 86 " 0.024 5.00e-02 4.00e+02 ... (remaining 4353 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.09: 10 2.09 - 2.79: 5361 2.79 - 3.49: 35279 3.49 - 4.20: 58330 4.20 - 4.90: 102540 Nonbonded interactions: 201520 Sorted by model distance: nonbonded pdb=" OE2 GLU A 212 " pdb=" OG SER A 222 " model vdw 1.382 2.440 nonbonded pdb=" OE1 GLU C 212 " pdb=" CB LEU C 224 " model vdw 1.822 3.440 nonbonded pdb=" OE1 GLU E 152 " pdb=" NZ LYS F 99 " model vdw 1.927 2.520 nonbonded pdb=" OD2 ASP F 124 " pdb=" NZ LYS G 119 " model vdw 1.945 2.520 nonbonded pdb=" OE2 GLU E 188 " pdb=" OG SER F 62 " model vdw 2.025 2.440 ... (remaining 201515 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' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'B' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'C' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'D' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'E' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'F' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 80 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 118 or (resid 119 and \ (name N or name CA or name C or name O or name CB )) or resid 120 through 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 13 through 216 or (resid 217 and (name N or name CA or name C or name O or name \ CB )) or resid 218 through 224 or (resid 225 and (name N or name CA or name C or \ name O or name CB )) or resid 226 through 275)) selection = (chain 'G' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'H' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 211 or ( \ resid 212 and (name N or name CA or name C or name O or name CB )) or resid 213 \ through 275)) selection = (chain 'I' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'J' and (resid 19 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 80 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 118 or (resid 119 and \ (name N or name CA or name C or name O or name CB )) or resid 120 through 216 o \ r (resid 217 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 18 through 224 or (resid 225 and (name N or name CA or name C or name O or name \ CB )) or resid 226 through 275)) selection = (chain 'K' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 118 or (resid 119 and \ (name N or name CA or name C or name O or name CB )) or resid 120 through 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 13 through 216 or (resid 217 and (name N or name CA or name C or name O or name \ CB )) or resid 218 through 224 or (resid 225 and (name N or name CA or name C or \ name O or name CB )) or resid 226 through 275)) selection = (chain 'L' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 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: 0.030 Extract box with map and model: 5.220 Check model and map are aligned: 0.410 Set scattering table: 0.300 Process input model: 72.570 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 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 : 0.003 0.081 26664 Z= 0.175 Angle : 0.659 27.054 36129 Z= 0.379 Chirality : 0.044 0.795 4072 Planarity : 0.004 0.066 4356 Dihedral : 14.972 175.485 10650 Min Nonbonded Distance : 1.382 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.65 % Favored : 97.25 % Rotamer: Outliers : 0.11 % Allowed : 3.69 % Favored : 96.20 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.14), residues: 3060 helix: 0.25 (0.11), residues: 1810 sheet: 0.73 (0.36), residues: 204 loop : -0.05 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 20 HIS 0.005 0.001 HIS K 77 PHE 0.008 0.001 PHE H 204 TYR 0.011 0.001 TYR J 93 ARG 0.004 0.000 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1423 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1420 time to evaluate : 3.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ILE cc_start: 0.7690 (mt) cc_final: 0.6636 (tp) REVERT: A 129 THR cc_start: 0.8523 (m) cc_final: 0.8190 (t) REVERT: A 229 MET cc_start: 0.3554 (mtp) cc_final: 0.3192 (mpp) REVERT: B 107 LYS cc_start: 0.9036 (mtpt) cc_final: 0.8626 (mtmm) REVERT: C 46 LEU cc_start: 0.8938 (mt) cc_final: 0.8706 (mt) REVERT: C 144 ASP cc_start: 0.7536 (t70) cc_final: 0.6965 (t0) REVERT: C 173 THR cc_start: 0.7704 (p) cc_final: 0.7062 (t) REVERT: C 196 PHE cc_start: 0.7620 (t80) cc_final: 0.6894 (t80) REVERT: D 100 CYS cc_start: 0.7833 (t) cc_final: 0.7627 (t) REVERT: D 141 LEU cc_start: 0.9466 (tp) cc_final: 0.9245 (tt) REVERT: D 159 ASP cc_start: 0.7892 (m-30) cc_final: 0.7619 (m-30) REVERT: E 156 ASP cc_start: 0.7928 (m-30) cc_final: 0.7508 (m-30) REVERT: G 71 ASP cc_start: 0.6116 (m-30) cc_final: 0.5602 (m-30) REVERT: H 93 TYR cc_start: 0.7811 (t80) cc_final: 0.7332 (t80) REVERT: H 127 ASP cc_start: 0.7890 (m-30) cc_final: 0.7655 (m-30) REVERT: H 156 ASP cc_start: 0.7235 (m-30) cc_final: 0.7033 (m-30) REVERT: H 159 ASP cc_start: 0.7100 (m-30) cc_final: 0.6827 (m-30) REVERT: I 99 LYS cc_start: 0.7410 (mttt) cc_final: 0.7022 (mttm) REVERT: I 170 LEU cc_start: 0.9291 (mt) cc_final: 0.9060 (mt) REVERT: I 198 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7892 (mtmt) REVERT: I 232 ILE cc_start: 0.8159 (mt) cc_final: 0.7870 (tt) REVERT: J 93 TYR cc_start: 0.7404 (t80) cc_final: 0.7135 (t80) REVERT: J 123 SER cc_start: 0.8816 (p) cc_final: 0.8560 (p) REVERT: J 144 ASP cc_start: 0.8272 (t0) cc_final: 0.7819 (t0) REVERT: J 176 LEU cc_start: 0.8847 (tp) cc_final: 0.8510 (tt) REVERT: K 46 LEU cc_start: 0.8224 (mt) cc_final: 0.7813 (mt) REVERT: L 190 PHE cc_start: 0.6452 (m-80) cc_final: 0.6220 (m-80) outliers start: 3 outliers final: 2 residues processed: 1421 average time/residue: 0.4153 time to fit residues: 874.4152 Evaluate side-chains 718 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 716 time to evaluate : 3.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain I residue 77 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 3.9990 chunk 230 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 238 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 177 optimal weight: 0.8980 chunk 276 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 HIS ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 GLN ** H 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 223 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 GLN I 213 GLN I 223 ASN J 38 GLN ** L 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 HIS L 206 ASN L 269 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 26664 Z= 0.346 Angle : 0.796 11.718 36129 Z= 0.400 Chirality : 0.045 0.298 4072 Planarity : 0.005 0.060 4356 Dihedral : 16.031 175.429 4199 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.09 % Favored : 97.84 % Rotamer: Outliers : 4.85 % Allowed : 19.28 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.14), residues: 3060 helix: 0.78 (0.12), residues: 1810 sheet: 1.05 (0.27), residues: 314 loop : 0.32 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP F 211 HIS 0.017 0.002 HIS L 43 PHE 0.021 0.002 PHE B 204 TYR 0.038 0.002 TYR A 75 ARG 0.011 0.001 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 732 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 THR cc_start: 0.8320 (m) cc_final: 0.8003 (t) REVERT: D 159 ASP cc_start: 0.8024 (m-30) cc_final: 0.7797 (m-30) REVERT: E 132 VAL cc_start: 0.9329 (t) cc_final: 0.9111 (p) REVERT: E 210 MET cc_start: 0.6867 (ttm) cc_final: 0.6403 (mtp) REVERT: F 99 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8574 (mtpp) REVERT: F 232 ILE cc_start: 0.8304 (mt) cc_final: 0.7944 (tp) REVERT: I 170 LEU cc_start: 0.9371 (mt) cc_final: 0.9105 (mt) REVERT: I 232 ILE cc_start: 0.8472 (mt) cc_final: 0.8192 (tt) REVERT: K 112 TYR cc_start: 0.9024 (t80) cc_final: 0.8608 (t80) REVERT: K 140 MET cc_start: 0.5767 (ttp) cc_final: 0.4931 (ttp) outliers start: 130 outliers final: 78 residues processed: 813 average time/residue: 0.3725 time to fit residues: 469.9442 Evaluate side-chains 694 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 616 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 70 CYS Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain G residue 20 TRP Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 240 TYR Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 269 GLN Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 246 GLU Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 HIS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 264 ASP Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain K residue 22 GLN Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 223 ASN Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 235 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 5.9990 chunk 85 optimal weight: 0.3980 chunk 229 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 276 optimal weight: 6.9990 chunk 298 optimal weight: 0.9980 chunk 246 optimal weight: 1.9990 chunk 274 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 221 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN B 223 ASN D 185 GLN E 22 GLN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 GLN ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 HIS ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26664 Z= 0.274 Angle : 0.746 13.016 36129 Z= 0.373 Chirality : 0.044 0.241 4072 Planarity : 0.004 0.050 4356 Dihedral : 15.856 176.483 4197 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.32 % Favored : 97.61 % Rotamer: Outliers : 5.00 % Allowed : 20.40 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.15), residues: 3060 helix: 0.98 (0.12), residues: 1799 sheet: 1.30 (0.28), residues: 314 loop : 0.45 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 211 HIS 0.021 0.001 HIS A 43 PHE 0.018 0.002 PHE L 196 TYR 0.035 0.002 TYR L 75 ARG 0.012 0.001 ARG G 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 641 time to evaluate : 5.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 THR cc_start: 0.8363 (m) cc_final: 0.8030 (t) REVERT: A 157 VAL cc_start: 0.9034 (m) cc_final: 0.8782 (m) REVERT: A 185 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.8006 (mm-40) REVERT: B 159 ASP cc_start: 0.7979 (t70) cc_final: 0.7763 (t0) REVERT: B 179 VAL cc_start: 0.8501 (p) cc_final: 0.8128 (m) REVERT: C 80 GLN cc_start: 0.8019 (tp-100) cc_final: 0.7759 (tp-100) REVERT: D 104 ASP cc_start: 0.7490 (p0) cc_final: 0.7241 (p0) REVERT: D 196 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8255 (m-80) REVERT: F 81 GLN cc_start: 0.6790 (tp40) cc_final: 0.6518 (mm110) REVERT: I 232 ILE cc_start: 0.8396 (mt) cc_final: 0.8157 (tt) REVERT: K 271 VAL cc_start: 0.8416 (t) cc_final: 0.7742 (t) REVERT: L 99 LYS cc_start: 0.7926 (mppt) cc_final: 0.7568 (mppt) outliers start: 134 outliers final: 99 residues processed: 721 average time/residue: 0.3801 time to fit residues: 429.2958 Evaluate side-chains 660 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 559 time to evaluate : 3.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 70 CYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain C residue 70 CYS Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 70 CYS Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 98 GLN Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 240 TYR Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 269 GLN Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 246 GLU Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 HIS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 264 ASP Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 163 ASP Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 221 SER Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 223 ASN Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 235 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 185 optimal weight: 0.8980 chunk 277 optimal weight: 0.7980 chunk 293 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 263 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 GLN H 213 GLN I 22 GLN I 37 GLN ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 97 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.6044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26664 Z= 0.205 Angle : 0.730 10.897 36129 Z= 0.363 Chirality : 0.044 0.201 4072 Planarity : 0.004 0.050 4356 Dihedral : 15.718 174.092 4197 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.09 % Favored : 97.84 % Rotamer: Outliers : 4.48 % Allowed : 21.93 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.15), residues: 3060 helix: 1.11 (0.12), residues: 1740 sheet: 1.41 (0.28), residues: 314 loop : 0.08 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 211 HIS 0.009 0.001 HIS A 43 PHE 0.016 0.001 PHE A 196 TYR 0.040 0.001 TYR L 75 ARG 0.006 0.000 ARG K 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 618 time to evaluate : 3.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 THR cc_start: 0.8347 (m) cc_final: 0.8032 (t) REVERT: B 159 ASP cc_start: 0.7928 (t70) cc_final: 0.7709 (t0) REVERT: C 46 LEU cc_start: 0.9041 (mt) cc_final: 0.8798 (mp) REVERT: D 104 ASP cc_start: 0.7556 (p0) cc_final: 0.7326 (p0) REVERT: D 179 VAL cc_start: 0.9021 (t) cc_final: 0.8780 (p) REVERT: G 115 TYR cc_start: 0.8150 (m-10) cc_final: 0.7806 (m-10) REVERT: I 232 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8135 (tt) REVERT: L 98 GLN cc_start: 0.7522 (mm-40) cc_final: 0.6351 (mp10) REVERT: L 133 LEU cc_start: 0.8788 (tp) cc_final: 0.8549 (tt) outliers start: 120 outliers final: 82 residues processed: 685 average time/residue: 0.3552 time to fit residues: 385.0487 Evaluate side-chains 624 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 541 time to evaluate : 3.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 70 CYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 269 GLN Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 70 CYS Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 240 TYR Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 269 GLN Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 213 GLN Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 HIS Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 264 ASP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 223 ASN Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 263 ILE Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 235 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 chunk 250 optimal weight: 10.0000 chunk 203 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 150 optimal weight: 40.0000 chunk 263 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.6436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26664 Z= 0.298 Angle : 0.741 13.757 36129 Z= 0.373 Chirality : 0.044 0.217 4072 Planarity : 0.004 0.053 4356 Dihedral : 15.630 168.516 4197 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.16 % Favored : 97.68 % Rotamer: Outliers : 5.18 % Allowed : 21.97 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.15), residues: 3060 helix: 1.08 (0.12), residues: 1743 sheet: 1.56 (0.26), residues: 347 loop : 0.15 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K 211 HIS 0.006 0.001 HIS A 43 PHE 0.017 0.002 PHE K 190 TYR 0.016 0.001 TYR B 73 ARG 0.009 0.000 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 552 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 THR cc_start: 0.8392 (m) cc_final: 0.8096 (t) REVERT: B 179 VAL cc_start: 0.8833 (m) cc_final: 0.8628 (p) REVERT: C 154 PHE cc_start: 0.8627 (m-80) cc_final: 0.8423 (m-80) REVERT: C 185 GLN cc_start: 0.7088 (mp10) cc_final: 0.5850 (mp10) REVERT: D 104 ASP cc_start: 0.7565 (p0) cc_final: 0.7284 (p0) REVERT: D 179 VAL cc_start: 0.9149 (t) cc_final: 0.8916 (p) REVERT: D 196 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8264 (m-80) REVERT: G 229 MET cc_start: 0.1350 (mtt) cc_final: 0.1017 (mtt) REVERT: I 232 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8112 (tt) REVERT: L 37 GLN cc_start: 0.7350 (pm20) cc_final: 0.7104 (pm20) REVERT: L 98 GLN cc_start: 0.7038 (mm-40) cc_final: 0.6742 (mp10) REVERT: L 99 LYS cc_start: 0.8136 (mmmt) cc_final: 0.7886 (tptt) REVERT: L 133 LEU cc_start: 0.8796 (tp) cc_final: 0.8545 (tt) REVERT: L 157 VAL cc_start: 0.9414 (t) cc_final: 0.9138 (p) outliers start: 139 outliers final: 97 residues processed: 635 average time/residue: 0.3496 time to fit residues: 352.1298 Evaluate side-chains 596 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 497 time to evaluate : 3.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 70 CYS Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 70 CYS Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 269 GLN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 98 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 204 PHE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 HIS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 264 ASP Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 140 MET Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 223 ASN Chi-restraints excluded: chain K residue 263 ILE Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 235 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 294 optimal weight: 0.7980 chunk 244 optimal weight: 0.6980 chunk 136 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 154 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 HIS F 213 GLN ** G 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 GLN ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.6640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26664 Z= 0.209 Angle : 0.741 12.683 36129 Z= 0.367 Chirality : 0.044 0.336 4072 Planarity : 0.004 0.056 4356 Dihedral : 15.464 172.677 4197 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.12 % Favored : 97.68 % Rotamer: Outliers : 4.63 % Allowed : 23.20 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.15), residues: 3060 helix: 1.11 (0.13), residues: 1717 sheet: 1.65 (0.27), residues: 347 loop : 0.14 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K 211 HIS 0.006 0.001 HIS A 43 PHE 0.016 0.001 PHE C 196 TYR 0.026 0.001 TYR G 75 ARG 0.011 0.000 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 551 time to evaluate : 3.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.6525 (tpp) cc_final: 0.6232 (tpt) REVERT: B 179 VAL cc_start: 0.8834 (m) cc_final: 0.8606 (p) REVERT: C 185 GLN cc_start: 0.6658 (mp10) cc_final: 0.6156 (mp10) REVERT: C 196 PHE cc_start: 0.7924 (t80) cc_final: 0.7462 (t80) REVERT: D 104 ASP cc_start: 0.7653 (p0) cc_final: 0.7417 (p0) REVERT: D 159 ASP cc_start: 0.7927 (m-30) cc_final: 0.7701 (m-30) REVERT: D 196 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8233 (m-80) REVERT: E 187 LEU cc_start: 0.9079 (pp) cc_final: 0.8861 (tt) REVERT: E 213 GLN cc_start: 0.7265 (pp30) cc_final: 0.7025 (pp30) REVERT: F 81 GLN cc_start: 0.6284 (OUTLIER) cc_final: 0.6058 (mm110) REVERT: G 158 ARG cc_start: 0.7428 (ttp80) cc_final: 0.6054 (tmm-80) REVERT: H 213 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.6653 (pp30) REVERT: L 37 GLN cc_start: 0.7334 (pm20) cc_final: 0.7127 (pm20) REVERT: L 98 GLN cc_start: 0.6962 (mm-40) cc_final: 0.6360 (mp10) REVERT: L 133 LEU cc_start: 0.8760 (tp) cc_final: 0.8542 (tt) REVERT: L 157 VAL cc_start: 0.9401 (t) cc_final: 0.9160 (p) REVERT: L 176 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7869 (tt) outliers start: 124 outliers final: 89 residues processed: 621 average time/residue: 0.3515 time to fit residues: 349.1819 Evaluate side-chains 599 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 506 time to evaluate : 3.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 70 CYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 70 CYS Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 269 GLN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 204 PHE Chi-restraints excluded: chain F residue 211 TRP Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 213 GLN Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 HIS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 264 ASP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 163 ASP Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 223 ASN Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 263 ILE Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 204 PHE Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 230 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 214 optimal weight: 0.9990 chunk 166 optimal weight: 0.5980 chunk 247 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 293 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.6803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26664 Z= 0.205 Angle : 0.756 19.970 36129 Z= 0.373 Chirality : 0.044 0.259 4072 Planarity : 0.004 0.056 4356 Dihedral : 15.367 174.893 4197 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.42 % Favored : 97.35 % Rotamer: Outliers : 4.10 % Allowed : 23.80 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.15), residues: 3060 helix: 1.12 (0.13), residues: 1707 sheet: 1.46 (0.28), residues: 314 loop : -0.04 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP K 211 HIS 0.007 0.001 HIS A 43 PHE 0.026 0.001 PHE H 204 TYR 0.015 0.001 TYR A 240 ARG 0.009 0.000 ARG L 254 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 539 time to evaluate : 5.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 104 ASP cc_start: 0.7657 (p0) cc_final: 0.7404 (p0) REVERT: D 159 ASP cc_start: 0.7897 (m-30) cc_final: 0.7656 (m-30) REVERT: D 179 VAL cc_start: 0.9080 (t) cc_final: 0.8843 (p) REVERT: D 196 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8168 (m-80) REVERT: E 159 ASP cc_start: 0.8563 (t0) cc_final: 0.8348 (t0) REVERT: F 81 GLN cc_start: 0.6180 (OUTLIER) cc_final: 0.5830 (mm110) REVERT: G 269 GLN cc_start: 0.5787 (OUTLIER) cc_final: 0.5539 (pm20) REVERT: L 37 GLN cc_start: 0.7254 (pm20) cc_final: 0.7042 (pm20) REVERT: L 133 LEU cc_start: 0.8775 (tp) cc_final: 0.8560 (tt) REVERT: L 157 VAL cc_start: 0.9426 (t) cc_final: 0.9153 (p) REVERT: L 176 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7880 (tt) outliers start: 110 outliers final: 89 residues processed: 598 average time/residue: 0.3381 time to fit residues: 323.6962 Evaluate side-chains 595 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 502 time to evaluate : 3.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 70 CYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 70 CYS Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 269 GLN Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 98 GLN Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 211 TRP Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 269 GLN Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 152 GLU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 275 TYR Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 HIS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 264 ASP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 163 ASP Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 223 ASN Chi-restraints excluded: chain K residue 263 ILE Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 204 PHE Chi-restraints excluded: chain L residue 210 MET Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 230 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 0.0020 chunk 117 optimal weight: 0.9990 chunk 174 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 199 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 230 optimal weight: 2.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 GLN ** L 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.6971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 26664 Z= 0.200 Angle : 0.765 15.180 36129 Z= 0.378 Chirality : 0.045 0.334 4072 Planarity : 0.004 0.057 4356 Dihedral : 15.213 176.244 4197 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.48 % Favored : 97.29 % Rotamer: Outliers : 4.03 % Allowed : 24.17 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.15), residues: 3060 helix: 1.12 (0.13), residues: 1695 sheet: 1.74 (0.30), residues: 292 loop : 0.01 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 211 HIS 0.007 0.001 HIS A 43 PHE 0.029 0.001 PHE C 196 TYR 0.037 0.001 TYR G 75 ARG 0.011 0.000 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 551 time to evaluate : 3.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ILE cc_start: 0.7060 (mm) cc_final: 0.6820 (mm) REVERT: D 104 ASP cc_start: 0.7414 (p0) cc_final: 0.7127 (p0) REVERT: D 159 ASP cc_start: 0.7849 (m-30) cc_final: 0.7643 (m-30) REVERT: D 179 VAL cc_start: 0.9063 (t) cc_final: 0.8834 (p) REVERT: D 196 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8155 (m-80) REVERT: F 81 GLN cc_start: 0.6322 (OUTLIER) cc_final: 0.5905 (mm110) REVERT: F 211 TRP cc_start: 0.6190 (OUTLIER) cc_final: 0.5918 (t60) REVERT: I 275 TYR cc_start: 0.6812 (m-80) cc_final: 0.6147 (m-10) REVERT: J 275 TYR cc_start: 0.6387 (m-80) cc_final: 0.6154 (m-80) REVERT: K 140 MET cc_start: 0.7974 (ppp) cc_final: 0.7115 (ppp) REVERT: L 133 LEU cc_start: 0.8794 (tp) cc_final: 0.8499 (tt) REVERT: L 176 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8023 (tt) outliers start: 108 outliers final: 85 residues processed: 609 average time/residue: 0.3462 time to fit residues: 337.7648 Evaluate side-chains 606 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 517 time to evaluate : 3.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 70 CYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 70 CYS Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 269 GLN Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 98 GLN Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 211 TRP Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 275 TYR Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 HIS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain I residue 264 ASP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 163 ASP Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 223 ASN Chi-restraints excluded: chain K residue 263 ILE Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 204 PHE Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 268 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 3.9990 chunk 280 optimal weight: 0.2980 chunk 256 optimal weight: 0.9990 chunk 273 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 246 optimal weight: 4.9990 chunk 258 optimal weight: 0.9980 chunk 272 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.7134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 26664 Z= 0.208 Angle : 0.801 15.239 36129 Z= 0.392 Chirality : 0.045 0.354 4072 Planarity : 0.004 0.057 4356 Dihedral : 15.085 176.704 4197 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.42 % Favored : 97.32 % Rotamer: Outliers : 3.62 % Allowed : 25.62 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.15), residues: 3060 helix: 1.11 (0.13), residues: 1695 sheet: 1.76 (0.30), residues: 293 loop : -0.08 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP K 211 HIS 0.007 0.001 HIS A 43 PHE 0.033 0.001 PHE H 204 TYR 0.019 0.001 TYR I 275 ARG 0.010 0.000 ARG A 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 537 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ILE cc_start: 0.6920 (mm) cc_final: 0.6675 (mm) REVERT: D 104 ASP cc_start: 0.7381 (p0) cc_final: 0.7101 (p0) REVERT: D 118 THR cc_start: 0.8599 (m) cc_final: 0.8252 (p) REVERT: D 179 VAL cc_start: 0.9037 (t) cc_final: 0.8828 (p) REVERT: D 196 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8449 (m-80) REVERT: F 81 GLN cc_start: 0.6367 (OUTLIER) cc_final: 0.6016 (mm110) REVERT: F 196 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.7114 (m-80) REVERT: F 211 TRP cc_start: 0.6182 (OUTLIER) cc_final: 0.5911 (t60) REVERT: H 162 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7369 (mt-10) REVERT: L 133 LEU cc_start: 0.8777 (tp) cc_final: 0.8486 (tt) outliers start: 97 outliers final: 81 residues processed: 590 average time/residue: 0.3553 time to fit residues: 339.0789 Evaluate side-chains 589 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 504 time to evaluate : 3.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 56 CYS Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 70 CYS Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 269 GLN Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 211 TRP Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 HIS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain I residue 264 ASP Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 163 ASP Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 223 ASN Chi-restraints excluded: chain K residue 263 ILE Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 268 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 0.0970 chunk 288 optimal weight: 0.9980 chunk 176 optimal weight: 0.2980 chunk 136 optimal weight: 7.9990 chunk 200 optimal weight: 10.0000 chunk 302 optimal weight: 6.9990 chunk 278 optimal weight: 9.9990 chunk 241 optimal weight: 0.9980 chunk 25 optimal weight: 30.0000 chunk 186 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 GLN ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.7269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 26664 Z= 0.205 Angle : 0.827 17.826 36129 Z= 0.402 Chirality : 0.046 0.384 4072 Planarity : 0.004 0.063 4356 Dihedral : 14.921 178.182 4197 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.45 % Favored : 97.29 % Rotamer: Outliers : 3.43 % Allowed : 26.33 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.15), residues: 3060 helix: 1.03 (0.13), residues: 1696 sheet: 1.75 (0.30), residues: 292 loop : -0.09 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 211 HIS 0.007 0.001 HIS A 43 PHE 0.025 0.001 PHE F 204 TYR 0.041 0.001 TYR G 75 ARG 0.012 0.000 ARG B 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 541 time to evaluate : 3.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 104 ASP cc_start: 0.7337 (p0) cc_final: 0.7027 (p0) REVERT: D 118 THR cc_start: 0.8548 (m) cc_final: 0.8228 (p) REVERT: D 179 VAL cc_start: 0.9034 (t) cc_final: 0.8798 (p) REVERT: D 196 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8379 (m-80) REVERT: F 81 GLN cc_start: 0.6344 (OUTLIER) cc_final: 0.6026 (mm110) REVERT: F 196 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.6806 (m-80) REVERT: F 211 TRP cc_start: 0.6306 (OUTLIER) cc_final: 0.5976 (t60) REVERT: G 190 PHE cc_start: 0.7508 (m-10) cc_final: 0.7268 (m-80) REVERT: H 162 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7184 (mt-10) REVERT: L 37 GLN cc_start: 0.7221 (pm20) cc_final: 0.6994 (pm20) REVERT: L 133 LEU cc_start: 0.8745 (tp) cc_final: 0.8466 (tt) outliers start: 92 outliers final: 80 residues processed: 588 average time/residue: 0.3537 time to fit residues: 331.5618 Evaluate side-chains 600 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 516 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 70 CYS Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 269 GLN Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 98 GLN Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 211 TRP Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 HIS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain I residue 264 ASP Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 163 ASP Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 223 ASN Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 263 ILE Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 5.9990 chunk 256 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 chunk 35 optimal weight: 0.0270 chunk 67 optimal weight: 6.9990 chunk 241 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.089318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.061501 restraints weight = 96167.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.063608 restraints weight = 50882.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.064988 restraints weight = 33371.133| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.7409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 26664 Z= 0.253 Angle : 0.827 15.830 36129 Z= 0.408 Chirality : 0.046 0.366 4072 Planarity : 0.004 0.057 4356 Dihedral : 14.785 179.641 4197 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.48 % Favored : 97.25 % Rotamer: Outliers : 3.54 % Allowed : 26.67 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.15), residues: 3060 helix: 1.09 (0.13), residues: 1696 sheet: 1.51 (0.26), residues: 348 loop : -0.11 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 211 HIS 0.007 0.001 HIS A 43 PHE 0.031 0.002 PHE F 204 TYR 0.025 0.001 TYR B 93 ARG 0.017 0.000 ARG K 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7010.29 seconds wall clock time: 131 minutes 28.31 seconds (7888.31 seconds total)