Starting phenix.real_space_refine on Mon Feb 19 23:37:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9a_23721/02_2024/7m9a_23721_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9a_23721/02_2024/7m9a_23721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9a_23721/02_2024/7m9a_23721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9a_23721/02_2024/7m9a_23721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9a_23721/02_2024/7m9a_23721_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9a_23721/02_2024/7m9a_23721_updated.pdb" } resolution = 3.9 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= 0.004 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: 13.91, 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: 10.73 Conformation dependent library (CDL) restraints added in 4.5 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: 10.48 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: 3.527A 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: 3.651A 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: 3.533A 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: 4.251A 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: 4.893A 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: 3.614A 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: 3.729A 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: 3.608A 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: 4.454A 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: 3.934A 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: 3.649A pdb=" N LYS F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 4.017A 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: 3.765A 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: 3.955A 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: 3.583A 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: 3.756A 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: 4.186A 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: 4.137A 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: 3.653A pdb=" N LYS H 273 " --> pdb=" O GLN H 269 " (cutoff:3.500A) removed outlier: 3.660A 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: 3.534A 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: 3.657A pdb=" N GLN I 213 " --> pdb=" O GLU I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 237 removed outlier: 3.505A 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: 3.535A 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: 3.883A 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: 3.555A 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: 3.654A 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: 3.922A 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: 4.376A 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: 3.869A 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: 7.313A 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: 3.565A 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: 6.742A 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: 6.746A 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: 7.567A 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: 6.986A 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: 8.077A 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: 8.36 Time building geometry restraints manager: 11.31 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: 7507 1.34 - 1.45: 3784 1.45 - 1.57: 15093 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 1.487 -0.030 1.41e-02 5.03e+03 4.48e+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 3.92e+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 1.98e+00 bond pdb=" CA ARG C 85 " pdb=" C ARG C 85 " ideal model delta sigma weight residual 1.524 1.539 -0.015 1.26e-02 6.30e+03 1.42e+00 ... (remaining 26659 not shown) Histogram of bond angle deviations from ideal: 92.04 - 101.00: 50 101.00 - 109.97: 3656 109.97 - 118.93: 18790 118.93 - 127.90: 13418 127.90 - 136.87: 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 98.32 16.43 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 109.81 136.87 -27.06 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 110.56 132.86 -22.30 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 92.97 16.99 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 92.04 18.33 1.78e+00 3.16e-01 1.06e+02 ... (remaining 36124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 15972 35.09 - 70.17: 434 70.17 - 105.26: 13 105.26 - 140.34: 9 140.34 - 175.43: 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 -60.00 115.43 -175.43 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 300.00 128.25 171.75 1 2.00e+01 2.50e-03 4.78e+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 -60.00 101.86 -161.86 1 2.00e+01 2.50e-03 4.68e+01 ... (remaining 16431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 4056 0.160 - 0.319: 13 0.319 - 0.479: 1 0.479 - 0.638: 1 0.638 - 0.798: 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 1.59e+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 9.02e+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 3.48e+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 6.60e-02 6.96e+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 3.29e+00 pdb=" N PRO D 86 " 0.078 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 4.31e-02 2.97e+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 - 2.08: 6 2.08 - 2.79: 5333 2.79 - 3.49: 35271 3.49 - 4.20: 58327 4.20 - 4.90: 102506 Nonbonded interactions: 201443 Sorted by model distance: nonbonded pdb=" OE2 GLU A 212 " pdb=" OG SER A 222 " model vdw 1.381 2.440 nonbonded pdb=" OE1 GLU C 212 " pdb=" CB LEU C 224 " model vdw 1.821 3.440 nonbonded pdb=" NE ARG F 53 " pdb=" OE2 GLU F 139 " model vdw 2.046 2.520 nonbonded pdb=" O VAL K 89 " pdb=" N VAL K 138 " model vdw 2.059 2.520 nonbonded pdb=" OE1 GLU E 61 " pdb=" OH TYR E 240 " model vdw 2.063 2.440 ... (remaining 201438 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: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 5.090 Check model and map are aligned: 0.400 Set scattering table: 0.260 Process input model: 73.960 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 88.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 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= 0.173 Angle : 0.658 27.056 36129 Z= 0.379 Chirality : 0.044 0.798 4072 Planarity : 0.004 0.066 4356 Dihedral : 15.027 175.428 10650 Min Nonbonded Distance : 1.381 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.65 % Favored : 97.25 % Rotamer: Outliers : 0.11 % Allowed : 3.69 % Favored : 96.20 % Cbeta Deviations : 0.14 % 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 G 196 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 916 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 913 time to evaluate : 3.062 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: A 166 ILE cc_start: 0.7578 (mt) cc_final: 0.7377 (pt) REVERT: A 210 MET cc_start: 0.0946 (ttt) cc_final: 0.0700 (tpp) REVERT: B 25 ILE cc_start: 0.5586 (mm) cc_final: 0.5236 (pt) REVERT: B 55 SER cc_start: 0.8339 (m) cc_final: 0.8064 (p) REVERT: B 67 THR cc_start: 0.5079 (m) cc_final: 0.4375 (m) REVERT: B 100 CYS cc_start: 0.7608 (t) cc_final: 0.7237 (t) REVERT: B 171 VAL cc_start: 0.8377 (t) cc_final: 0.8147 (p) REVERT: C 55 SER cc_start: 0.9379 (m) cc_final: 0.8968 (t) REVERT: C 156 ASP cc_start: 0.8016 (m-30) cc_final: 0.7783 (m-30) REVERT: C 159 ASP cc_start: 0.7625 (m-30) cc_final: 0.7160 (m-30) REVERT: C 163 ASP cc_start: 0.7943 (m-30) cc_final: 0.7674 (m-30) REVERT: D 85 ARG cc_start: 0.5851 (ttp-110) cc_final: 0.4834 (ptt180) REVERT: D 123 SER cc_start: 0.8602 (m) cc_final: 0.8252 (p) REVERT: E 114 LYS cc_start: 0.8723 (mttt) cc_final: 0.8335 (mmtt) REVERT: E 153 THR cc_start: 0.8754 (p) cc_final: 0.8374 (t) REVERT: E 204 PHE cc_start: 0.8867 (t80) cc_final: 0.8651 (t80) REVERT: E 205 LYS cc_start: 0.7412 (mtmt) cc_final: 0.6591 (ptmm) REVERT: E 268 LEU cc_start: 0.8931 (tp) cc_final: 0.8464 (tp) REVERT: F 104 ASP cc_start: 0.7730 (m-30) cc_final: 0.7192 (t70) REVERT: F 157 VAL cc_start: 0.9137 (t) cc_final: 0.8825 (p) REVERT: F 207 THR cc_start: 0.8420 (m) cc_final: 0.8005 (p) REVERT: F 211 TRP cc_start: 0.7363 (m100) cc_final: 0.6761 (m100) REVERT: F 275 TYR cc_start: 0.2682 (t80) cc_final: 0.1713 (t80) REVERT: G 75 TYR cc_start: 0.6351 (m-10) cc_final: 0.5946 (m-10) REVERT: G 88 THR cc_start: 0.6973 (m) cc_final: 0.6336 (t) REVERT: G 142 ILE cc_start: 0.8844 (mm) cc_final: 0.8439 (mm) REVERT: H 104 ASP cc_start: 0.7941 (m-30) cc_final: 0.7325 (t0) REVERT: H 271 VAL cc_start: 0.8111 (t) cc_final: 0.7686 (t) REVERT: I 59 VAL cc_start: 0.8845 (t) cc_final: 0.8615 (m) REVERT: I 210 MET cc_start: 0.8123 (ttp) cc_final: 0.7781 (ttm) REVERT: J 139 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7645 (mt-10) REVERT: K 99 LYS cc_start: 0.8485 (mttt) cc_final: 0.8195 (tppt) REVERT: K 114 LYS cc_start: 0.8338 (mttt) cc_final: 0.8123 (mmtt) REVERT: K 156 ASP cc_start: 0.6588 (m-30) cc_final: 0.6189 (m-30) REVERT: K 176 LEU cc_start: 0.8222 (tp) cc_final: 0.7885 (tp) REVERT: L 38 GLN cc_start: 0.7186 (mm-40) cc_final: 0.6697 (pt0) REVERT: L 41 THR cc_start: 0.5684 (m) cc_final: 0.5000 (m) REVERT: L 42 LEU cc_start: 0.6904 (tp) cc_final: 0.6439 (tp) REVERT: L 95 ARG cc_start: 0.6322 (ptm160) cc_final: 0.6120 (ptm-80) REVERT: L 99 LYS cc_start: 0.7243 (mttt) cc_final: 0.7018 (ttmm) REVERT: L 229 MET cc_start: 0.3616 (mtt) cc_final: 0.2621 (mmp) REVERT: L 274 GLU cc_start: 0.4948 (tt0) cc_final: 0.4641 (tp30) outliers start: 3 outliers final: 0 residues processed: 916 average time/residue: 0.4723 time to fit residues: 617.6577 Evaluate side-chains 407 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 407 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.0570 chunk 230 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 144 optimal weight: 0.0670 chunk 177 optimal weight: 0.6980 chunk 276 optimal weight: 4.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 HIS B 185 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 GLN D 269 GLN E 213 GLN F 223 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 ASN K 185 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26664 Z= 0.209 Angle : 0.655 8.602 36129 Z= 0.323 Chirality : 0.041 0.189 4072 Planarity : 0.005 0.059 4356 Dihedral : 16.049 177.361 4195 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.99 % Favored : 97.94 % Rotamer: Outliers : 2.76 % Allowed : 10.89 % Favored : 86.35 % 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: 1.22 (0.15), residues: 3060 helix: 1.09 (0.12), residues: 1809 sheet: 1.07 (0.37), residues: 204 loop : 0.48 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 45 HIS 0.005 0.001 HIS K 43 PHE 0.013 0.001 PHE F 204 TYR 0.025 0.001 TYR G 73 ARG 0.010 0.001 ARG H 243 *********************** 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 513 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 439 time to evaluate : 3.126 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: A 63 ARG cc_start: 0.2971 (mmp-170) cc_final: 0.2205 (mmp-170) REVERT: A 141 LEU cc_start: 0.6464 (tp) cc_final: 0.5998 (pp) REVERT: A 245 ASP cc_start: 0.4024 (m-30) cc_final: 0.3411 (m-30) REVERT: B 38 GLN cc_start: 0.6998 (tp40) cc_final: 0.6355 (mm-40) REVERT: B 152 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6537 (tm-30) REVERT: C 55 SER cc_start: 0.9310 (m) cc_final: 0.9066 (t) REVERT: C 85 ARG cc_start: 0.5053 (OUTLIER) cc_final: 0.4724 (ptt90) REVERT: C 159 ASP cc_start: 0.7420 (m-30) cc_final: 0.6573 (m-30) REVERT: D 213 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7599 (mm-40) REVERT: D 214 MET cc_start: 0.7685 (mmm) cc_final: 0.7483 (mtt) REVERT: D 273 LYS cc_start: 0.8322 (mttt) cc_final: 0.7916 (mtmm) REVERT: E 75 TYR cc_start: 0.7085 (m-10) cc_final: 0.6821 (m-10) REVERT: E 114 LYS cc_start: 0.8756 (mttt) cc_final: 0.8365 (mmtt) REVERT: E 140 MET cc_start: 0.7981 (ttm) cc_final: 0.7768 (tpp) REVERT: F 78 LYS cc_start: 0.7949 (mttp) cc_final: 0.7341 (mmmt) REVERT: F 244 LEU cc_start: 0.9200 (tp) cc_final: 0.8991 (tp) REVERT: G 70 CYS cc_start: 0.6347 (t) cc_final: 0.5337 (t) REVERT: G 75 TYR cc_start: 0.6159 (m-10) cc_final: 0.5848 (m-10) REVERT: H 139 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7450 (mp0) REVERT: I 59 VAL cc_start: 0.8831 (t) cc_final: 0.8479 (m) REVERT: I 123 SER cc_start: 0.8227 (OUTLIER) cc_final: 0.7871 (t) REVERT: J 127 ASP cc_start: 0.7441 (m-30) cc_final: 0.7239 (m-30) REVERT: K 73 TYR cc_start: 0.8800 (t80) cc_final: 0.8562 (t80) REVERT: K 99 LYS cc_start: 0.8631 (mttt) cc_final: 0.8374 (tptp) REVERT: K 114 LYS cc_start: 0.8316 (mttt) cc_final: 0.8056 (mmtt) REVERT: K 176 LEU cc_start: 0.8374 (tp) cc_final: 0.8018 (tp) REVERT: L 38 GLN cc_start: 0.7191 (mm-40) cc_final: 0.6829 (pt0) REVERT: L 68 VAL cc_start: 0.7461 (OUTLIER) cc_final: 0.7237 (p) outliers start: 74 outliers final: 41 residues processed: 495 average time/residue: 0.4246 time to fit residues: 315.3441 Evaluate side-chains 388 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 343 time to evaluate : 2.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 212 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 223 ASN Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 157 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 229 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 276 optimal weight: 7.9990 chunk 298 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 274 optimal weight: 9.9990 chunk 94 optimal weight: 0.5980 chunk 221 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 HIS ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN H 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 26664 Z= 0.243 Angle : 0.621 8.040 36129 Z= 0.306 Chirality : 0.041 0.223 4072 Planarity : 0.004 0.059 4356 Dihedral : 16.035 177.284 4195 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.42 % Favored : 97.52 % Rotamer: Outliers : 3.69 % Allowed : 12.57 % Favored : 83.74 % 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: 1.32 (0.15), residues: 3060 helix: 1.25 (0.12), residues: 1832 sheet: 1.04 (0.36), residues: 204 loop : 0.36 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J 45 HIS 0.004 0.001 HIS A 43 PHE 0.026 0.001 PHE J 204 TYR 0.022 0.001 TYR G 73 ARG 0.010 0.001 ARG C 85 *********************** 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 474 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 375 time to evaluate : 3.244 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: A 63 ARG cc_start: 0.3198 (mmp-170) cc_final: 0.2596 (mmp-170) REVERT: A 229 MET cc_start: 0.1138 (mmm) cc_final: 0.0734 (mmm) REVERT: A 245 ASP cc_start: 0.3862 (m-30) cc_final: 0.3465 (m-30) REVERT: B 38 GLN cc_start: 0.7033 (tp40) cc_final: 0.6596 (mm-40) REVERT: B 152 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7097 (tm-30) REVERT: B 184 GLU cc_start: 0.6892 (pp20) cc_final: 0.6493 (pp20) REVERT: C 55 SER cc_start: 0.9323 (m) cc_final: 0.9073 (t) REVERT: D 116 ARG cc_start: 0.8537 (ttm-80) cc_final: 0.7925 (mtt-85) REVERT: D 214 MET cc_start: 0.7663 (mmm) cc_final: 0.7455 (mtt) REVERT: D 256 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8623 (mp) REVERT: D 273 LYS cc_start: 0.8469 (mttt) cc_final: 0.8125 (mtmm) REVERT: E 37 GLN cc_start: 0.7393 (tp-100) cc_final: 0.7180 (tp-100) REVERT: E 75 TYR cc_start: 0.7273 (m-10) cc_final: 0.6930 (m-10) REVERT: E 114 LYS cc_start: 0.8699 (mttt) cc_final: 0.8375 (mmtt) REVERT: E 205 LYS cc_start: 0.8075 (mtmt) cc_final: 0.7679 (mmtp) REVERT: F 78 LYS cc_start: 0.7871 (mttp) cc_final: 0.7296 (mmmt) REVERT: F 210 MET cc_start: 0.7299 (tpt) cc_final: 0.7043 (tpp) REVERT: F 211 TRP cc_start: 0.7808 (m100) cc_final: 0.7413 (m100) REVERT: G 140 MET cc_start: 0.8102 (mmm) cc_final: 0.7835 (tpp) REVERT: H 139 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7682 (mp0) REVERT: I 59 VAL cc_start: 0.8911 (t) cc_final: 0.8541 (m) REVERT: I 123 SER cc_start: 0.8430 (OUTLIER) cc_final: 0.8006 (t) REVERT: I 229 MET cc_start: 0.6905 (mmp) cc_final: 0.6464 (mmp) REVERT: K 73 TYR cc_start: 0.8903 (t80) cc_final: 0.8673 (t80) REVERT: K 99 LYS cc_start: 0.8629 (mttt) cc_final: 0.8344 (tptp) REVERT: K 114 LYS cc_start: 0.8444 (mttt) cc_final: 0.8193 (mmtt) REVERT: K 176 LEU cc_start: 0.8367 (tp) cc_final: 0.8056 (tp) REVERT: K 177 ASP cc_start: 0.7560 (t70) cc_final: 0.7093 (t0) REVERT: K 187 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8096 (mt) REVERT: L 38 GLN cc_start: 0.7323 (mm-40) cc_final: 0.6900 (pt0) REVERT: L 104 ASP cc_start: 0.7595 (m-30) cc_final: 0.7150 (t0) REVERT: L 145 GLU cc_start: 0.6576 (mm-30) cc_final: 0.6260 (mm-30) outliers start: 99 outliers final: 67 residues processed: 455 average time/residue: 0.4066 time to fit residues: 289.6983 Evaluate side-chains 383 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 312 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 85 ARG Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain H residue 212 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 223 ASN Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 223 ASN Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 157 VAL Chi-restraints excluded: chain L residue 208 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 185 optimal weight: 2.9990 chunk 277 optimal weight: 10.0000 chunk 293 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN H 38 GLN I 185 GLN L 213 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 26664 Z= 0.314 Angle : 0.649 7.942 36129 Z= 0.323 Chirality : 0.042 0.195 4072 Planarity : 0.005 0.058 4356 Dihedral : 16.108 179.464 4195 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.39 % Rotamer: Outliers : 4.36 % Allowed : 14.66 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.15), residues: 3060 helix: 1.27 (0.12), residues: 1805 sheet: 0.81 (0.35), residues: 205 loop : 0.08 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 45 HIS 0.005 0.001 HIS I 77 PHE 0.014 0.002 PHE H 125 TYR 0.019 0.002 TYR G 73 ARG 0.011 0.001 ARG C 231 *********************** 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 459 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 342 time to evaluate : 3.742 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: A 245 ASP cc_start: 0.3839 (m-30) cc_final: 0.3456 (m-30) REVERT: B 38 GLN cc_start: 0.6997 (tp40) cc_final: 0.6623 (mm-40) REVERT: B 112 TYR cc_start: 0.9239 (t80) cc_final: 0.9026 (t80) REVERT: B 152 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7351 (tm-30) REVERT: B 241 ILE cc_start: 0.8490 (mm) cc_final: 0.8209 (mm) REVERT: C 175 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7455 (ttm110) REVERT: D 116 ARG cc_start: 0.8537 (ttm-80) cc_final: 0.7844 (mtt-85) REVERT: D 214 MET cc_start: 0.7959 (mmm) cc_final: 0.7672 (mtt) REVERT: D 273 LYS cc_start: 0.8528 (mttt) cc_final: 0.8174 (mtmm) REVERT: E 114 LYS cc_start: 0.8661 (mttt) cc_final: 0.8299 (mmtm) REVERT: E 205 LYS cc_start: 0.8085 (mtmt) cc_final: 0.7709 (mmtp) REVERT: F 78 LYS cc_start: 0.7890 (mttp) cc_final: 0.7250 (mmmt) REVERT: F 214 MET cc_start: 0.6803 (mmt) cc_final: 0.6591 (mmm) REVERT: G 210 MET cc_start: 0.6448 (mtt) cc_final: 0.6013 (mmp) REVERT: G 214 MET cc_start: 0.5424 (mmp) cc_final: 0.4341 (tpt) REVERT: I 78 LYS cc_start: 0.8386 (mttt) cc_final: 0.8099 (mttm) REVERT: I 118 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8420 (p) REVERT: I 123 SER cc_start: 0.8483 (OUTLIER) cc_final: 0.7994 (t) REVERT: I 226 SER cc_start: 0.6781 (OUTLIER) cc_final: 0.6151 (m) REVERT: J 104 ASP cc_start: 0.7800 (m-30) cc_final: 0.7132 (t0) REVERT: J 139 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7602 (mt-10) REVERT: K 73 TYR cc_start: 0.9060 (t80) cc_final: 0.8832 (t80) REVERT: K 99 LYS cc_start: 0.8633 (mttt) cc_final: 0.8230 (tppt) REVERT: K 176 LEU cc_start: 0.8303 (tp) cc_final: 0.8071 (tp) REVERT: K 177 ASP cc_start: 0.7674 (t70) cc_final: 0.7357 (t0) REVERT: K 187 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8094 (mt) REVERT: L 104 ASP cc_start: 0.7860 (m-30) cc_final: 0.7171 (t0) outliers start: 117 outliers final: 80 residues processed: 435 average time/residue: 0.3898 time to fit residues: 260.5106 Evaluate side-chains 391 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 305 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain G residue 45 TRP Chi-restraints excluded: chain G residue 56 CYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 85 ARG Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 CYS Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain H residue 212 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 223 ASN Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 221 SER Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 223 ASN Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 157 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 218 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 250 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 263 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN H 38 GLN I 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 26664 Z= 0.306 Angle : 0.630 7.666 36129 Z= 0.315 Chirality : 0.042 0.183 4072 Planarity : 0.005 0.062 4356 Dihedral : 15.946 178.730 4195 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.78 % Favored : 97.16 % Rotamer: Outliers : 4.59 % Allowed : 15.59 % Favored : 79.82 % 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: 1.03 (0.15), residues: 3060 helix: 1.17 (0.12), residues: 1840 sheet: 0.73 (0.35), residues: 205 loop : -0.07 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 45 HIS 0.008 0.001 HIS A 43 PHE 0.015 0.002 PHE H 125 TYR 0.017 0.001 TYR G 73 ARG 0.006 0.001 ARG L 76 *********************** 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 451 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 328 time to evaluate : 3.006 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: A 40 LYS cc_start: 0.5535 (OUTLIER) cc_final: 0.5237 (ptpp) REVERT: A 43 HIS cc_start: 0.6703 (m-70) cc_final: 0.6302 (m-70) REVERT: A 182 ARG cc_start: 0.4505 (tpm170) cc_final: 0.3977 (ttm-80) REVERT: B 104 ASP cc_start: 0.7425 (t70) cc_final: 0.7002 (t0) REVERT: B 112 TYR cc_start: 0.9334 (t80) cc_final: 0.9107 (t80) REVERT: C 85 ARG cc_start: 0.5088 (OUTLIER) cc_final: 0.4154 (ptt90) REVERT: C 175 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7534 (ttm110) REVERT: D 116 ARG cc_start: 0.8520 (ttm-80) cc_final: 0.7863 (mtt-85) REVERT: D 229 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7421 (mtm) REVERT: D 273 LYS cc_start: 0.8792 (mttt) cc_final: 0.8387 (mtmm) REVERT: E 114 LYS cc_start: 0.8665 (mttt) cc_final: 0.8282 (mmtm) REVERT: E 205 LYS cc_start: 0.8139 (mtmt) cc_final: 0.7769 (mmtp) REVERT: F 78 LYS cc_start: 0.7860 (mttp) cc_final: 0.7261 (mmmt) REVERT: G 85 ARG cc_start: 0.4685 (OUTLIER) cc_final: 0.4407 (mtm110) REVERT: G 175 ARG cc_start: 0.7624 (mmm-85) cc_final: 0.7281 (tpp80) REVERT: G 210 MET cc_start: 0.6448 (mtt) cc_final: 0.5870 (mtp) REVERT: I 118 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8481 (p) REVERT: I 123 SER cc_start: 0.8443 (OUTLIER) cc_final: 0.7936 (t) REVERT: I 226 SER cc_start: 0.7066 (OUTLIER) cc_final: 0.6322 (m) REVERT: J 104 ASP cc_start: 0.7691 (m-30) cc_final: 0.6982 (t0) REVERT: J 139 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7311 (mt-10) REVERT: K 99 LYS cc_start: 0.8625 (mttt) cc_final: 0.8217 (tppt) REVERT: K 187 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8063 (mt) REVERT: L 104 ASP cc_start: 0.7848 (m-30) cc_final: 0.7169 (t0) REVERT: L 225 LYS cc_start: 0.4477 (OUTLIER) cc_final: 0.4270 (mtmm) outliers start: 123 outliers final: 84 residues processed: 421 average time/residue: 0.3952 time to fit residues: 256.6768 Evaluate side-chains 385 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 291 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 211 TRP Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain G residue 45 TRP Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 85 ARG Chi-restraints excluded: chain G residue 93 TYR Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 CYS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 212 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 223 ASN Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 153 THR Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 223 ASN Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain K residue 24 GLU Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 157 VAL Chi-restraints excluded: chain L residue 225 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 172 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 294 optimal weight: 9.9990 chunk 244 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 97 optimal weight: 0.6980 chunk 154 optimal weight: 9.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN H 38 GLN I 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26664 Z= 0.283 Angle : 0.622 7.704 36129 Z= 0.309 Chirality : 0.041 0.206 4072 Planarity : 0.004 0.058 4356 Dihedral : 15.749 179.441 4195 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.04 % Favored : 96.90 % Rotamer: Outliers : 4.63 % Allowed : 16.56 % Favored : 78.81 % 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: 1.17 (0.12), residues: 1840 sheet: 0.72 (0.35), residues: 205 loop : -0.10 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 45 HIS 0.005 0.001 HIS A 43 PHE 0.016 0.001 PHE H 125 TYR 0.017 0.001 TYR G 112 ARG 0.009 0.000 ARG D 27 *********************** 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 439 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 315 time to evaluate : 3.135 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: A 182 ARG cc_start: 0.4588 (tpm170) cc_final: 0.4118 (ttm-80) REVERT: B 104 ASP cc_start: 0.7410 (t70) cc_final: 0.6952 (t0) REVERT: B 112 TYR cc_start: 0.9353 (t80) cc_final: 0.9149 (t80) REVERT: B 196 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.6534 (t80) REVERT: C 85 ARG cc_start: 0.5131 (OUTLIER) cc_final: 0.4137 (ptt90) REVERT: C 175 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7553 (ttm110) REVERT: D 116 ARG cc_start: 0.8526 (ttm-80) cc_final: 0.7850 (mtt-85) REVERT: D 273 LYS cc_start: 0.8829 (mttt) cc_final: 0.8396 (mtmm) REVERT: E 114 LYS cc_start: 0.8687 (mttt) cc_final: 0.8312 (mmtm) REVERT: E 205 LYS cc_start: 0.8202 (mtmt) cc_final: 0.7840 (mmtp) REVERT: F 78 LYS cc_start: 0.7833 (mttp) cc_final: 0.7240 (mmmt) REVERT: G 85 ARG cc_start: 0.4689 (OUTLIER) cc_final: 0.4348 (mtm110) REVERT: G 175 ARG cc_start: 0.7695 (mmm-85) cc_final: 0.7385 (tpp80) REVERT: G 210 MET cc_start: 0.6584 (mtt) cc_final: 0.6351 (mmm) REVERT: H 62 SER cc_start: 0.8504 (OUTLIER) cc_final: 0.8272 (p) REVERT: I 118 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8541 (p) REVERT: I 123 SER cc_start: 0.8488 (OUTLIER) cc_final: 0.8010 (t) REVERT: I 226 SER cc_start: 0.7043 (OUTLIER) cc_final: 0.6269 (m) REVERT: J 51 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8103 (mppt) REVERT: J 104 ASP cc_start: 0.7703 (m-30) cc_final: 0.6987 (t0) REVERT: J 139 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7521 (mt-10) REVERT: K 71 ASP cc_start: 0.8146 (t0) cc_final: 0.7809 (t0) REVERT: K 99 LYS cc_start: 0.8630 (mttt) cc_final: 0.8354 (tptp) REVERT: L 104 ASP cc_start: 0.7847 (m-30) cc_final: 0.7355 (t0) outliers start: 124 outliers final: 88 residues processed: 412 average time/residue: 0.4058 time to fit residues: 259.6650 Evaluate side-chains 381 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 284 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 211 TRP Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 85 ARG Chi-restraints excluded: chain G residue 93 TYR Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 CYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain H residue 212 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 223 ASN Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 140 MET Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 223 ASN Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain K residue 24 GLU Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 157 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 0.9980 chunk 33 optimal weight: 0.0870 chunk 167 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 293 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.5902 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= 0.174 Angle : 0.578 9.624 36129 Z= 0.282 Chirality : 0.040 0.354 4072 Planarity : 0.004 0.045 4356 Dihedral : 15.460 178.862 4195 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 3.43 % Allowed : 17.90 % Favored : 78.66 % 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: 1.25 (0.15), residues: 3060 helix: 1.43 (0.12), residues: 1817 sheet: 0.81 (0.34), residues: 213 loop : -0.13 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 20 HIS 0.004 0.001 HIS A 43 PHE 0.037 0.001 PHE F 204 TYR 0.012 0.001 TYR G 73 ARG 0.005 0.000 ARG D 27 *********************** 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 408 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 316 time to evaluate : 3.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 HIS cc_start: 0.6676 (m-70) cc_final: 0.6292 (m-70) REVERT: A 182 ARG cc_start: 0.4586 (tpm170) cc_final: 0.4142 (ttm-80) REVERT: B 104 ASP cc_start: 0.7461 (t70) cc_final: 0.6953 (t0) REVERT: B 112 TYR cc_start: 0.9337 (t80) cc_final: 0.9116 (t80) REVERT: B 196 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.6361 (t80) REVERT: C 175 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7482 (ttm110) REVERT: D 31 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7904 (ptpp) REVERT: D 116 ARG cc_start: 0.8502 (ttm-80) cc_final: 0.8208 (ttm110) REVERT: D 119 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8495 (tppt) REVERT: D 273 LYS cc_start: 0.8795 (mttt) cc_final: 0.8359 (mtmm) REVERT: E 114 LYS cc_start: 0.8698 (mttt) cc_final: 0.8388 (mmtt) REVERT: E 139 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6602 (mp0) REVERT: E 205 LYS cc_start: 0.8159 (mtmt) cc_final: 0.7784 (mmtp) REVERT: F 78 LYS cc_start: 0.7851 (mttp) cc_final: 0.7252 (mmmt) REVERT: F 210 MET cc_start: 0.7283 (tpp) cc_final: 0.7054 (tpp) REVERT: G 210 MET cc_start: 0.6568 (mtt) cc_final: 0.6218 (mtp) REVERT: I 118 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8495 (p) REVERT: I 123 SER cc_start: 0.8455 (OUTLIER) cc_final: 0.8059 (t) REVERT: J 139 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7587 (mt-10) REVERT: K 99 LYS cc_start: 0.8619 (mttt) cc_final: 0.8369 (tptp) REVERT: L 73 TYR cc_start: 0.7539 (t80) cc_final: 0.7153 (t80) REVERT: L 104 ASP cc_start: 0.7882 (m-30) cc_final: 0.7338 (t0) outliers start: 92 outliers final: 59 residues processed: 383 average time/residue: 0.3854 time to fit residues: 229.2989 Evaluate side-chains 355 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 291 time to evaluate : 3.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 212 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 223 ASN Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 140 MET Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 186 VAL Chi-restraints excluded: chain I residue 221 SER Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 174 ASP Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 223 ASN Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 149 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 174 optimal weight: 20.0000 chunk 88 optimal weight: 0.3980 chunk 57 optimal weight: 0.5980 chunk 56 optimal weight: 0.2980 chunk 186 optimal weight: 0.8980 chunk 199 optimal weight: 9.9990 chunk 144 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 230 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN I 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26664 Z= 0.163 Angle : 0.565 7.456 36129 Z= 0.277 Chirality : 0.039 0.233 4072 Planarity : 0.004 0.078 4356 Dihedral : 15.258 178.643 4195 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.55 % Favored : 97.42 % Rotamer: Outliers : 3.06 % Allowed : 18.20 % Favored : 78.74 % 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: 1.38 (0.15), residues: 3060 helix: 1.64 (0.12), residues: 1796 sheet: 0.88 (0.34), residues: 213 loop : -0.26 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 211 HIS 0.005 0.001 HIS A 43 PHE 0.024 0.001 PHE C 204 TYR 0.032 0.001 TYR G 93 ARG 0.007 0.000 ARG C 85 *********************** 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 390 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 308 time to evaluate : 2.792 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: A 43 HIS cc_start: 0.6669 (m-70) cc_final: 0.6272 (m-70) REVERT: A 182 ARG cc_start: 0.4318 (tpm170) cc_final: 0.4028 (ttm-80) REVERT: B 104 ASP cc_start: 0.7441 (t70) cc_final: 0.6936 (t0) REVERT: B 112 TYR cc_start: 0.9333 (t80) cc_final: 0.9092 (t80) REVERT: B 196 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.6369 (t80) REVERT: C 175 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7467 (ttm110) REVERT: D 31 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7893 (ptpp) REVERT: D 116 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.8222 (ttm110) REVERT: D 119 LYS cc_start: 0.8760 (mmmt) cc_final: 0.8494 (tppt) REVERT: D 273 LYS cc_start: 0.8799 (mttt) cc_final: 0.8369 (mtmm) REVERT: E 114 LYS cc_start: 0.8705 (mttt) cc_final: 0.8399 (mmtt) REVERT: E 205 LYS cc_start: 0.8139 (mtmt) cc_final: 0.7811 (mmtp) REVERT: E 230 LEU cc_start: 0.8208 (tt) cc_final: 0.7858 (mt) REVERT: F 78 LYS cc_start: 0.7805 (mttp) cc_final: 0.7212 (mmmt) REVERT: G 210 MET cc_start: 0.6610 (mtt) cc_final: 0.6248 (mtp) REVERT: I 118 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8477 (p) REVERT: I 123 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8010 (t) REVERT: J 139 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7730 (mt-10) REVERT: K 99 LYS cc_start: 0.8604 (mttt) cc_final: 0.8371 (tptp) REVERT: L 73 TYR cc_start: 0.7529 (t80) cc_final: 0.7094 (t80) REVERT: L 104 ASP cc_start: 0.7933 (m-30) cc_final: 0.7309 (t0) outliers start: 82 outliers final: 62 residues processed: 367 average time/residue: 0.3902 time to fit residues: 220.6099 Evaluate side-chains 354 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 287 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 70 CYS Chi-restraints excluded: chain G residue 85 ARG Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 212 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 223 ASN Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 140 MET Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 221 SER Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 174 ASP Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 223 ASN Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 225 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 5.9990 chunk 280 optimal weight: 8.9990 chunk 256 optimal weight: 2.9990 chunk 273 optimal weight: 9.9990 chunk 164 optimal weight: 0.2980 chunk 118 optimal weight: 0.7980 chunk 214 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 246 optimal weight: 0.3980 chunk 258 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN C 43 HIS ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 GLN L 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.6141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26664 Z= 0.204 Angle : 0.595 10.071 36129 Z= 0.290 Chirality : 0.040 0.355 4072 Planarity : 0.004 0.082 4356 Dihedral : 15.234 177.071 4195 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.88 % Favored : 97.03 % Rotamer: Outliers : 3.13 % Allowed : 18.65 % Favored : 78.22 % 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: 1.36 (0.15), residues: 3060 helix: 1.63 (0.12), residues: 1796 sheet: 0.89 (0.33), residues: 212 loop : -0.29 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 20 HIS 0.005 0.001 HIS A 43 PHE 0.044 0.001 PHE F 204 TYR 0.016 0.001 TYR G 93 ARG 0.007 0.000 ARG F 258 *********************** 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 375 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 291 time to evaluate : 3.277 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: A 43 HIS cc_start: 0.6626 (m-70) cc_final: 0.6225 (m-70) REVERT: A 182 ARG cc_start: 0.4345 (tpm170) cc_final: 0.4066 (ttm-80) REVERT: B 104 ASP cc_start: 0.7492 (t70) cc_final: 0.6971 (t0) REVERT: B 112 TYR cc_start: 0.9346 (t80) cc_final: 0.9106 (t80) REVERT: B 196 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.6402 (t80) REVERT: B 206 ASN cc_start: 0.6943 (OUTLIER) cc_final: 0.6680 (t0) REVERT: C 175 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7544 (ttm110) REVERT: C 231 ARG cc_start: 0.7445 (ptt-90) cc_final: 0.7239 (ptp90) REVERT: D 31 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7897 (ptpp) REVERT: D 81 GLN cc_start: 0.6620 (OUTLIER) cc_final: 0.6295 (tm-30) REVERT: D 116 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.8229 (ttm110) REVERT: D 119 LYS cc_start: 0.8780 (mmmt) cc_final: 0.8512 (tppt) REVERT: D 273 LYS cc_start: 0.8821 (mttt) cc_final: 0.8392 (mtmm) REVERT: E 114 LYS cc_start: 0.8704 (mttt) cc_final: 0.8406 (mmtt) REVERT: E 205 LYS cc_start: 0.8151 (mtmt) cc_final: 0.7849 (mmtp) REVERT: E 230 LEU cc_start: 0.8233 (tt) cc_final: 0.7883 (mt) REVERT: F 78 LYS cc_start: 0.7802 (mttp) cc_final: 0.7206 (mmmt) REVERT: I 118 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8496 (p) REVERT: I 123 SER cc_start: 0.8454 (OUTLIER) cc_final: 0.8025 (t) REVERT: J 51 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8228 (mppt) REVERT: J 139 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7735 (mt-10) REVERT: K 99 LYS cc_start: 0.8596 (mttt) cc_final: 0.8369 (tptp) REVERT: L 73 TYR cc_start: 0.7527 (t80) cc_final: 0.7077 (t80) REVERT: L 104 ASP cc_start: 0.7943 (m-30) cc_final: 0.7320 (t0) outliers start: 84 outliers final: 67 residues processed: 352 average time/residue: 0.3675 time to fit residues: 203.2356 Evaluate side-chains 354 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 279 time to evaluate : 2.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 212 GLU Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 223 ASN Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 140 MET Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 221 SER Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 174 ASP Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 223 ASN Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 149 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 0.9980 chunk 288 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 200 optimal weight: 9.9990 chunk 302 optimal weight: 5.9990 chunk 278 optimal weight: 10.0000 chunk 241 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 GLN ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 GLN ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.6248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26664 Z= 0.211 Angle : 0.602 10.500 36129 Z= 0.292 Chirality : 0.041 0.336 4072 Planarity : 0.004 0.079 4356 Dihedral : 15.168 173.923 4195 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.07 % Favored : 96.83 % Rotamer: Outliers : 3.21 % Allowed : 18.65 % Favored : 78.14 % 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: 1.33 (0.15), residues: 3060 helix: 1.60 (0.12), residues: 1795 sheet: 0.93 (0.34), residues: 212 loop : -0.29 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 20 HIS 0.005 0.001 HIS A 43 PHE 0.018 0.001 PHE C 204 TYR 0.018 0.001 TYR G 93 ARG 0.005 0.000 ARG D 27 ********************** 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 375 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 289 time to evaluate : 2.837 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: A 43 HIS cc_start: 0.6645 (m-70) cc_final: 0.6243 (m-70) REVERT: A 182 ARG cc_start: 0.4419 (tpm170) cc_final: 0.4152 (ttm-80) REVERT: B 104 ASP cc_start: 0.7508 (t70) cc_final: 0.6983 (t0) REVERT: B 112 TYR cc_start: 0.9354 (t80) cc_final: 0.9123 (t80) REVERT: B 196 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.6421 (t80) REVERT: B 256 LEU cc_start: 0.5550 (mm) cc_final: 0.5188 (mt) REVERT: C 175 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7592 (ttm110) REVERT: D 31 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7879 (ptpp) REVERT: D 81 GLN cc_start: 0.6745 (OUTLIER) cc_final: 0.6133 (tm-30) REVERT: D 116 ARG cc_start: 0.8516 (ttm-80) cc_final: 0.8238 (ttm110) REVERT: D 119 LYS cc_start: 0.8804 (mmmt) cc_final: 0.8525 (tppt) REVERT: D 273 LYS cc_start: 0.8828 (mttt) cc_final: 0.8395 (mtmm) REVERT: E 114 LYS cc_start: 0.8720 (mttt) cc_final: 0.8410 (mmtt) REVERT: E 205 LYS cc_start: 0.8158 (mtmt) cc_final: 0.7856 (mmtp) REVERT: E 230 LEU cc_start: 0.8279 (tt) cc_final: 0.7976 (mt) REVERT: F 78 LYS cc_start: 0.7789 (mttp) cc_final: 0.7236 (mmmt) REVERT: I 118 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8506 (p) REVERT: I 123 SER cc_start: 0.8459 (OUTLIER) cc_final: 0.8021 (t) REVERT: J 51 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8235 (mppt) REVERT: J 139 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7767 (mt-10) REVERT: K 99 LYS cc_start: 0.8608 (mttt) cc_final: 0.8323 (tptp) REVERT: L 73 TYR cc_start: 0.7532 (t80) cc_final: 0.7108 (t80) REVERT: L 104 ASP cc_start: 0.7931 (m-30) cc_final: 0.7315 (t0) outliers start: 86 outliers final: 70 residues processed: 353 average time/residue: 0.3694 time to fit residues: 204.3629 Evaluate side-chains 349 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 272 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 70 CYS Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 212 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 223 ASN Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 140 MET Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 221 SER Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 174 ASP Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 223 ASN Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 149 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 0.0020 chunk 256 optimal weight: 0.0060 chunk 73 optimal weight: 10.0000 chunk 222 optimal weight: 4.9990 chunk 35 optimal weight: 0.0980 chunk 67 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.8206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 GLN ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.161236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.131246 restraints weight = 41505.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.133741 restraints weight = 82656.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.133743 restraints weight = 46155.622| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.6266 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= 0.221 Angle : 0.737 59.196 36129 Z= 0.390 Chirality : 0.044 1.032 4072 Planarity : 0.004 0.105 4356 Dihedral : 15.169 173.884 4195 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.01 % Favored : 96.86 % Rotamer: Outliers : 3.21 % Allowed : 18.61 % Favored : 78.18 % Cbeta Deviations : 0.03 % 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: 1.34 (0.15), residues: 3060 helix: 1.61 (0.12), residues: 1795 sheet: 0.93 (0.34), residues: 212 loop : -0.30 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 20 HIS 0.004 0.001 HIS A 43 PHE 0.017 0.001 PHE C 204 TYR 0.015 0.001 TYR G 93 ARG 0.009 0.000 ARG D 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5394.41 seconds wall clock time: 102 minutes 41.55 seconds (6161.55 seconds total)