Starting phenix.real_space_refine on Sun Apr 14 05:12:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9c_23723/04_2024/7m9c_23723_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9c_23723/04_2024/7m9c_23723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9c_23723/04_2024/7m9c_23723.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9c_23723/04_2024/7m9c_23723.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9c_23723/04_2024/7m9c_23723_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9c_23723/04_2024/7m9c_23723_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 86 5.49 5 S 112 5.16 5 C 19026 2.51 5 N 5552 2.21 5 O 5741 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 ASP 144": "OD1" <-> "OD2" 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" Residue "O TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 270": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 30517 Number of models: 1 Model: "" Number of chains: 26 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: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 693 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain breaks: 1 Chain: "N" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 660 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain breaks: 1 Chain: "O" 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: "P" 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: 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: 15.52, per 1000 atoms: 0.51 Number of scatterers: 30517 At special positions: 0 Unit cell: (195.51, 144.97, 172.9, 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 112 16.00 P 86 15.00 O 5741 8.00 N 5552 7.00 C 19026 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: 16.84 Conformation dependent library (CDL) restraints added in 5.3 seconds 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6748 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 175 helices and 16 sheets defined 55.0% alpha, 7.0% beta 30 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 13.45 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 removed outlier: 3.505A 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: 3.538A pdb=" N ASP A 71 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 112 Processing helix chain 'A' and resid 122 through 135 removed outlier: 3.528A pdb=" N LYS A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.538A 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: 3.797A 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: 3.565A pdb=" N ALA A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.898A 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: 3.570A 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: 3.868A 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: 4.036A pdb=" N GLU C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 3.787A 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: 3.728A pdb=" N ARG D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.608A 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: 3.554A 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: 3.510A pdb=" N ASP F 127 " --> pdb=" O SER F 123 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR F 129 " --> pdb=" O PHE F 125 " (cutoff:3.500A) removed outlier: 3.559A 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: 4.016A pdb=" N GLY F 135 " --> pdb=" O GLU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 163 removed outlier: 3.865A pdb=" N ALA F 155 " --> pdb=" O PRO F 151 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP F 156 " --> pdb=" O GLU F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 181 Processing helix chain 'F' and resid 184 through 189 Processing helix chain 'F' and resid 202 through 214 Processing helix chain 'F' and resid 227 through 237 Processing helix chain 'F' and resid 241 through 258 removed outlier: 3.765A 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: 3.552A 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: 4.694A 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: 3.908A 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: 3.586A pdb=" N VAL G 271 " --> pdb=" O VAL G 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA G 272 " --> pdb=" O LEU G 268 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS G 273 " --> pdb=" O GLN G 269 " (cutoff:3.500A) removed outlier: 4.278A 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: 4.187A pdb=" N LEU H 256 " --> pdb=" O ALA H 252 " (cutoff:3.500A) removed outlier: 4.288A 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: 3.767A 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: 3.659A pdb=" N GLU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 29 Processing helix chain 'I' and resid 37 through 52 Processing helix chain 'I' and resid 66 through 76 Processing helix chain 'I' and resid 104 through 112 Processing helix chain 'I' and resid 122 through 135 Processing helix chain 'I' and resid 146 through 148 No H-bonds generated for 'chain 'I' and resid 146 through 148' Processing helix chain 'I' and resid 151 through 163 removed outlier: 3.575A pdb=" N ALA I 155 " --> pdb=" O GLU I 152 " (cutoff:3.500A) removed outlier: 3.539A 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: 4.034A pdb=" N ARG I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 189 Processing helix chain 'I' and resid 201 through 214 removed outlier: 3.656A pdb=" N GLN I 213 " --> pdb=" O GLU I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 237 removed outlier: 3.505A 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: 3.979A pdb=" N ALA J 155 " --> pdb=" O PRO J 151 " (cutoff:3.500A) removed outlier: 3.884A 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: 4.292A 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: 3.921A pdb=" N ARG K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 112 Processing helix chain 'K' and resid 122 through 135 Processing helix chain 'K' and resid 146 through 148 No H-bonds generated for 'chain 'K' and resid 146 through 148' Processing helix chain 'K' and resid 153 through 163 Processing helix chain 'K' and resid 174 through 182 removed outlier: 3.880A pdb=" N ARG K 182 " --> pdb=" O ALA K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 189 Processing helix chain 'K' and resid 201 through 215 Processing helix chain 'K' and resid 227 through 237 Processing helix chain 'K' and resid 241 through 257 removed outlier: 4.371A 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: 3.612A 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: 4.065A 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: 3.645A pdb=" N VAL L 271 " --> pdb=" O VAL L 267 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA L 272 " --> pdb=" O LEU L 268 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS L 273 " --> pdb=" O GLN L 269 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 28 removed outlier: 3.504A pdb=" N LEU O 28 " --> pdb=" O GLU O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 52 Processing helix chain 'O' and resid 66 through 76 removed outlier: 3.537A pdb=" N ASP O 71 " --> pdb=" O THR O 67 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG O 76 " --> pdb=" O ALA O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 112 Processing helix chain 'O' and resid 122 through 135 removed outlier: 3.528A pdb=" N LYS O 134 " --> pdb=" O ILE O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 151 through 163 removed outlier: 3.537A pdb=" N PHE O 154 " --> pdb=" O PRO O 151 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG O 158 " --> pdb=" O ALA O 155 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA O 161 " --> pdb=" O ARG O 158 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP O 163 " --> pdb=" O ILE O 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 182 Processing helix chain 'O' and resid 184 through 187 No H-bonds generated for 'chain 'O' and resid 184 through 187' Processing helix chain 'O' and resid 201 through 215 Processing helix chain 'O' and resid 227 through 237 removed outlier: 3.893A pdb=" N ILE O 232 " --> pdb=" O GLU O 228 " (cutoff:3.500A) Processing helix chain 'O' and resid 241 through 258 Processing helix chain 'O' and resid 265 through 273 removed outlier: 3.564A pdb=" N ALA O 272 " --> pdb=" O LEU O 268 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS O 273 " --> pdb=" O GLN O 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 28 Processing helix chain 'P' and resid 37 through 52 Processing helix chain 'P' and resid 66 through 76 removed outlier: 3.551A pdb=" N ARG P 76 " --> pdb=" O ALA P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 112 Processing helix chain 'P' and resid 122 through 135 Processing helix chain 'P' and resid 154 through 163 Processing helix chain 'P' and resid 174 through 182 removed outlier: 3.955A pdb=" N ALA P 178 " --> pdb=" O ASP P 174 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL P 179 " --> pdb=" O ARG P 175 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 189 Processing helix chain 'P' and resid 201 through 214 Processing helix chain 'P' and resid 227 through 237 removed outlier: 3.904A pdb=" N ARG P 231 " --> pdb=" O LYS P 227 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE P 232 " --> pdb=" O GLU P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 241 through 257 Processing helix chain 'P' and resid 265 through 274 removed outlier: 3.907A pdb=" N GLN P 269 " --> pdb=" O LYS P 265 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU P 270 " --> pdb=" O ALA P 266 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL P 271 " --> pdb=" O VAL P 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA P 272 " --> pdb=" O LEU P 268 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS P 273 " --> pdb=" O GLN P 269 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU P 274 " --> pdb=" O GLU P 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 265 through 274' 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: 6.537A 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: 8.288A pdb=" N GLY F 172 " --> pdb=" O CYS F 56 " (cutoff:3.500A) removed outlier: 5.716A 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: 6.680A pdb=" N MET F 140 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 8.062A 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: 6.747A pdb=" N ARG H 57 " --> pdb=" O LEU H 194 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'I' and resid 193 through 196 removed outlier: 7.566A pdb=" N ARG I 57 " --> pdb=" O LEU I 194 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N PHE I 196 " --> pdb=" O ARG I 57 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL I 59 " --> pdb=" O PHE I 196 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'J' and resid 169 through 172 removed outlier: 6.986A 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: 8.078A pdb=" N ILE J 94 " --> pdb=" O MET J 140 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE J 142 " --> pdb=" O ILE J 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'K' and resid 193 through 195 removed outlier: 6.892A pdb=" N ARG K 57 " --> pdb=" O LEU K 194 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 193 through 195 removed outlier: 6.557A pdb=" N ARG L 57 " --> pdb=" O LEU L 194 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'O' and resid 193 through 195 removed outlier: 6.602A pdb=" N ARG O 57 " --> pdb=" O LEU O 194 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'P' and resid 193 through 195 removed outlier: 6.138A pdb=" N ARG P 57 " --> pdb=" O LEU P 194 " (cutoff:3.500A) 1319 hydrogen bonds defined for protein. 3771 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 10.94 Time building geometry restraints manager: 14.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 8097 1.33 - 1.45: 4985 1.45 - 1.57: 17724 1.57 - 1.69: 158 1.69 - 1.81: 168 Bond restraints: 31132 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 3.37e+01 bond pdb=" N LYS D 78 " pdb=" CA LYS D 78 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.41e-02 5.03e+03 4.28e+00 bond pdb=" CA LYS D 78 " pdb=" C LYS D 78 " ideal model delta sigma weight residual 1.524 1.548 -0.024 1.26e-02 6.30e+03 3.73e+00 bond pdb=" CB CYS H 56 " pdb=" SG CYS H 56 " ideal model delta sigma weight residual 1.808 1.761 0.047 3.30e-02 9.18e+02 1.99e+00 bond pdb=" C3' DT N -1 " pdb=" O3' DT N -1 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.60e+00 ... (remaining 31127 not shown) Histogram of bond angle deviations from ideal: 92.02 - 100.98: 57 100.98 - 109.94: 4183 109.94 - 118.90: 21997 118.90 - 127.87: 15690 127.87 - 136.83: 254 Bond angle restraints: 42181 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 98.31 16.44 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 109.81 136.83 -27.02 2.21e+00 2.05e-01 1.49e+02 angle pdb=" N THR C 173 " pdb=" CA THR C 173 " pdb=" C THR C 173 " ideal model delta sigma weight residual 110.56 132.84 -22.28 1.94e+00 2.66e-01 1.32e+02 angle pdb=" N LYS C 217 " pdb=" CA LYS C 217 " pdb=" C LYS C 217 " ideal model delta sigma weight residual 109.96 92.95 17.01 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 92.02 18.35 1.78e+00 3.16e-01 1.06e+02 ... (remaining 42176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 18644 35.09 - 70.18: 516 70.18 - 105.27: 15 105.27 - 140.36: 10 140.36 - 175.45: 5 Dihedral angle restraints: 19190 sinusoidal: 8760 harmonic: 10430 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 -60.00 115.45 -175.45 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 -60.00 101.89 -161.89 1 2.00e+01 2.50e-03 4.68e+01 ... (remaining 19187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 4735 0.160 - 0.319: 18 0.319 - 0.478: 1 0.478 - 0.638: 1 0.638 - 0.797: 1 Chirality restraints: 4756 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 8.94e+00 chirality pdb=" CA GLN C 81 " pdb=" N GLN C 81 " pdb=" C GLN C 81 " pdb=" CB GLN C 81 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 4753 not shown) Planarity restraints: 5084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 85 " -0.045 5.00e-02 4.00e+02 6.62e-02 7.02e+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 4.55e-02 3.31e+00 pdb=" N PRO D 86 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 86 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 86 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 85 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+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 5081 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 21 2.06 - 2.77: 4934 2.77 - 3.48: 41588 3.48 - 4.19: 68900 4.19 - 4.90: 121095 Nonbonded interactions: 236538 Sorted by model distance: nonbonded pdb=" CE1 HIS G 97 " pdb=" CZ ARG P 126 " model vdw 1.350 3.490 nonbonded pdb=" OE2 GLU O 212 " pdb=" OG SER O 222 " model vdw 1.381 2.440 nonbonded pdb=" OE2 GLU A 212 " pdb=" OG SER A 222 " model vdw 1.381 2.440 nonbonded pdb=" CE1 HIS G 97 " pdb=" NE ARG P 126 " model vdw 1.485 3.340 nonbonded pdb=" OD2 ASP F 124 " pdb=" NZ LYS G 119 " model vdw 1.589 2.520 ... (remaining 236533 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)) selection = (chain 'O' 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 'P' 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.190 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 88.180 Find NCS groups from input model: 2.600 Set up NCS constraints: 0.140 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 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 31132 Z= 0.174 Angle : 0.642 27.016 42181 Z= 0.372 Chirality : 0.043 0.797 4756 Planarity : 0.004 0.066 5084 Dihedral : 15.012 175.446 12442 Min Nonbonded Distance : 1.350 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.58 % Favored : 97.34 % Rotamer: Outliers : 0.10 % Allowed : 3.39 % Favored : 96.52 % Cbeta Deviations : 0.12 % 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: 0.09 (0.13), residues: 3570 helix: 0.20 (0.10), residues: 2100 sheet: 0.58 (0.33), residues: 238 loop : -0.00 (0.17), residues: 1232 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 P 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) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1833 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1830 time to evaluate : 3.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.9264 (mt) cc_final: 0.9060 (mt) REVERT: A 89 VAL cc_start: 0.7979 (t) cc_final: 0.7757 (t) REVERT: A 104 ASP cc_start: 0.8568 (m-30) cc_final: 0.8330 (m-30) REVERT: A 112 TYR cc_start: 0.8861 (t80) cc_final: 0.8412 (t80) REVERT: A 149 LEU cc_start: 0.9303 (tp) cc_final: 0.8963 (tp) REVERT: A 168 VAL cc_start: 0.9056 (t) cc_final: 0.8736 (p) REVERT: A 190 PHE cc_start: 0.8245 (m-80) cc_final: 0.7665 (m-80) REVERT: B 38 GLN cc_start: 0.8093 (tp40) cc_final: 0.7621 (tp40) REVERT: B 62 SER cc_start: 0.8494 (p) cc_final: 0.7689 (p) REVERT: B 156 ASP cc_start: 0.7630 (m-30) cc_final: 0.7252 (m-30) REVERT: C 25 ILE cc_start: 0.9110 (mt) cc_final: 0.8758 (pt) REVERT: C 147 ASP cc_start: 0.7574 (m-30) cc_final: 0.7180 (p0) REVERT: C 173 THR cc_start: 0.8137 (p) cc_final: 0.7592 (p) REVERT: C 253 ILE cc_start: 0.9111 (mt) cc_final: 0.8836 (mm) REVERT: D 28 LEU cc_start: 0.8571 (mt) cc_final: 0.8229 (mp) REVERT: D 247 ILE cc_start: 0.8791 (mt) cc_final: 0.8312 (mm) REVERT: E 113 LEU cc_start: 0.9336 (mt) cc_final: 0.9116 (mp) REVERT: E 144 ASP cc_start: 0.8395 (t70) cc_final: 0.6859 (t0) REVERT: E 159 ASP cc_start: 0.7549 (m-30) cc_final: 0.6617 (m-30) REVERT: E 247 ILE cc_start: 0.9552 (mt) cc_final: 0.8994 (mt) REVERT: E 253 ILE cc_start: 0.9376 (mt) cc_final: 0.9086 (pt) REVERT: F 190 PHE cc_start: 0.7986 (m-80) cc_final: 0.7735 (m-80) REVERT: F 207 THR cc_start: 0.8449 (m) cc_final: 0.8180 (m) REVERT: G 154 PHE cc_start: 0.8387 (m-80) cc_final: 0.8129 (m-80) REVERT: G 190 PHE cc_start: 0.8480 (m-80) cc_final: 0.8176 (m-80) REVERT: H 103 LYS cc_start: 0.9250 (tttt) cc_final: 0.8961 (pttt) REVERT: H 156 ASP cc_start: 0.8063 (m-30) cc_final: 0.7835 (m-30) REVERT: H 176 LEU cc_start: 0.9346 (tp) cc_final: 0.9114 (tt) REVERT: H 189 ARG cc_start: 0.8619 (tpt170) cc_final: 0.8095 (tpt90) REVERT: I 176 LEU cc_start: 0.9460 (tp) cc_final: 0.9129 (tp) REVERT: I 188 GLU cc_start: 0.7056 (tp30) cc_final: 0.6514 (tp30) REVERT: I 194 LEU cc_start: 0.9380 (mt) cc_final: 0.8488 (mt) REVERT: I 203 ASP cc_start: 0.7310 (m-30) cc_final: 0.6842 (m-30) REVERT: I 247 ILE cc_start: 0.9040 (mt) cc_final: 0.8794 (tp) REVERT: J 103 LYS cc_start: 0.8831 (tttt) cc_final: 0.8595 (tttm) REVERT: J 105 LEU cc_start: 0.9520 (tp) cc_final: 0.9178 (tp) REVERT: J 123 SER cc_start: 0.9103 (p) cc_final: 0.8585 (p) REVERT: J 138 VAL cc_start: 0.9357 (t) cc_final: 0.9042 (p) REVERT: J 144 ASP cc_start: 0.7134 (t0) cc_final: 0.6901 (t0) REVERT: K 49 LYS cc_start: 0.9166 (mmtm) cc_final: 0.8511 (mmmt) REVERT: K 108 LYS cc_start: 0.9153 (mttm) cc_final: 0.8917 (mttt) REVERT: K 144 ASP cc_start: 0.8064 (t0) cc_final: 0.7621 (t0) REVERT: K 156 ASP cc_start: 0.8611 (m-30) cc_final: 0.7510 (m-30) REVERT: K 247 ILE cc_start: 0.8935 (mt) cc_final: 0.8622 (tp) REVERT: L 100 CYS cc_start: 0.7734 (t) cc_final: 0.7190 (t) REVERT: L 166 ILE cc_start: 0.6801 (mt) cc_final: 0.6557 (pt) REVERT: O 46 LEU cc_start: 0.8225 (mt) cc_final: 0.7965 (mt) REVERT: O 86 PRO cc_start: 0.6670 (Cg_exo) cc_final: 0.6265 (Cg_endo) REVERT: O 130 ILE cc_start: 0.8926 (pt) cc_final: 0.8617 (pt) REVERT: O 232 ILE cc_start: 0.7454 (mt) cc_final: 0.6559 (pt) REVERT: P 42 LEU cc_start: 0.7346 (mt) cc_final: 0.7088 (mt) REVERT: P 106 PHE cc_start: 0.8523 (m-80) cc_final: 0.7771 (m-80) REVERT: P 144 ASP cc_start: 0.5929 (m-30) cc_final: 0.5717 (m-30) REVERT: P 190 PHE cc_start: 0.7237 (m-80) cc_final: 0.6940 (m-80) REVERT: P 214 MET cc_start: 0.5713 (mtt) cc_final: 0.5494 (tmm) REVERT: P 263 ILE cc_start: 0.3928 (mt) cc_final: 0.3720 (mp) outliers start: 3 outliers final: 2 residues processed: 1832 average time/residue: 0.5029 time to fit residues: 1361.7656 Evaluate side-chains 917 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 915 time to evaluate : 3.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 10.0000 chunk 269 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 182 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 chunk 279 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 chunk 207 optimal weight: 0.6980 chunk 323 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN H 223 ASN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 HIS ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 HIS ** P 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 31132 Z= 0.266 Angle : 0.720 10.839 42181 Z= 0.368 Chirality : 0.043 0.254 4756 Planarity : 0.005 0.054 5084 Dihedral : 16.056 177.258 4907 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.88 % Favored : 98.10 % Rotamer: Outliers : 0.35 % Allowed : 3.64 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.13), residues: 3570 helix: 0.66 (0.11), residues: 2028 sheet: 0.81 (0.26), residues: 358 loop : 0.35 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP P 211 HIS 0.020 0.001 HIS P 43 PHE 0.022 0.002 PHE J 204 TYR 0.023 0.002 TYR G 75 ARG 0.010 0.001 ARG D 182 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1149 time to evaluate : 3.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 46 LEU cc_start: 0.9392 (mt) cc_final: 0.9086 (mt) REVERT: A 136 CYS cc_start: 0.6855 (m) cc_final: 0.6275 (m) REVERT: A 149 LEU cc_start: 0.9293 (tp) cc_final: 0.9030 (tp) REVERT: B 46 LEU cc_start: 0.9246 (mt) cc_final: 0.8977 (mt) REVERT: B 190 PHE cc_start: 0.7567 (m-80) cc_final: 0.7181 (m-80) REVERT: B 194 LEU cc_start: 0.8603 (tp) cc_final: 0.8403 (tp) REVERT: C 46 LEU cc_start: 0.9344 (mt) cc_final: 0.9125 (mt) REVERT: C 133 LEU cc_start: 0.9616 (mt) cc_final: 0.9372 (mm) REVERT: C 210 MET cc_start: 0.6473 (tpt) cc_final: 0.5908 (tpt) REVERT: C 247 ILE cc_start: 0.8646 (mt) cc_final: 0.7309 (mt) REVERT: D 66 LYS cc_start: 0.8288 (pttt) cc_final: 0.8000 (pttt) REVERT: D 145 GLU cc_start: 0.7280 (pt0) cc_final: 0.6661 (pt0) REVERT: D 176 LEU cc_start: 0.9217 (tp) cc_final: 0.8929 (tp) REVERT: D 180 ILE cc_start: 0.8929 (mt) cc_final: 0.8649 (mt) REVERT: D 246 GLU cc_start: 0.7170 (pp20) cc_final: 0.6892 (pp20) REVERT: D 247 ILE cc_start: 0.8660 (mt) cc_final: 0.8216 (mm) REVERT: E 46 LEU cc_start: 0.9263 (mt) cc_final: 0.8950 (mt) REVERT: E 104 ASP cc_start: 0.7286 (t70) cc_final: 0.6681 (t0) REVERT: E 107 LYS cc_start: 0.8855 (tttp) cc_final: 0.8484 (ttmm) REVERT: E 247 ILE cc_start: 0.9477 (mt) cc_final: 0.9003 (mt) REVERT: E 275 TYR cc_start: 0.4598 (m-10) cc_final: 0.4048 (m-10) REVERT: F 36 LEU cc_start: 0.8465 (tt) cc_final: 0.7661 (tt) REVERT: F 144 ASP cc_start: 0.8170 (t70) cc_final: 0.7922 (t0) REVERT: F 145 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7556 (mt-10) REVERT: F 156 ASP cc_start: 0.8252 (m-30) cc_final: 0.7964 (m-30) REVERT: F 199 LEU cc_start: 0.7613 (tp) cc_final: 0.7089 (tp) REVERT: G 112 TYR cc_start: 0.8713 (t80) cc_final: 0.8490 (t80) REVERT: G 174 ASP cc_start: 0.6719 (p0) cc_final: 0.6275 (p0) REVERT: G 176 LEU cc_start: 0.8725 (tp) cc_final: 0.8411 (tp) REVERT: G 229 MET cc_start: 0.1917 (mtt) cc_final: 0.1513 (mtt) REVERT: H 103 LYS cc_start: 0.9179 (tttt) cc_final: 0.8912 (pttm) REVERT: H 112 TYR cc_start: 0.8372 (t80) cc_final: 0.8071 (t80) REVERT: H 156 ASP cc_start: 0.8644 (m-30) cc_final: 0.7834 (m-30) REVERT: H 176 LEU cc_start: 0.9390 (tp) cc_final: 0.9147 (tt) REVERT: I 93 TYR cc_start: 0.9110 (t80) cc_final: 0.8802 (t80) REVERT: I 130 ILE cc_start: 0.9396 (pt) cc_final: 0.9075 (mm) REVERT: J 112 TYR cc_start: 0.9095 (t80) cc_final: 0.8878 (t80) REVERT: J 232 ILE cc_start: 0.8906 (mm) cc_final: 0.8561 (tt) REVERT: K 37 GLN cc_start: 0.7811 (pm20) cc_final: 0.7074 (pm20) REVERT: K 46 LEU cc_start: 0.8940 (mt) cc_final: 0.8560 (mt) REVERT: K 158 ARG cc_start: 0.8106 (ptt90) cc_final: 0.7082 (ttp80) REVERT: K 240 TYR cc_start: 0.7337 (m-80) cc_final: 0.6017 (m-10) REVERT: K 253 ILE cc_start: 0.8500 (mm) cc_final: 0.8199 (mm) REVERT: L 25 ILE cc_start: 0.8391 (tt) cc_final: 0.7910 (tt) REVERT: L 100 CYS cc_start: 0.7829 (t) cc_final: 0.6922 (t) REVERT: L 105 LEU cc_start: 0.9077 (tp) cc_final: 0.8630 (tt) REVERT: L 180 ILE cc_start: 0.7352 (pt) cc_final: 0.6968 (pt) REVERT: L 185 GLN cc_start: 0.4369 (tm-30) cc_final: 0.3933 (tm-30) REVERT: L 190 PHE cc_start: 0.7211 (m-10) cc_final: 0.6994 (m-10) REVERT: O 71 ASP cc_start: 0.7161 (p0) cc_final: 0.6103 (p0) REVERT: O 106 PHE cc_start: 0.8407 (m-80) cc_final: 0.7740 (m-80) REVERT: O 142 ILE cc_start: 0.8692 (mp) cc_final: 0.8485 (mm) REVERT: P 106 PHE cc_start: 0.8702 (m-80) cc_final: 0.7785 (m-10) REVERT: P 168 VAL cc_start: 0.7722 (t) cc_final: 0.7521 (t) REVERT: P 232 ILE cc_start: 0.6304 (mm) cc_final: 0.6064 (mm) outliers start: 11 outliers final: 2 residues processed: 1155 average time/residue: 0.4702 time to fit residues: 837.4307 Evaluate side-chains 794 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 792 time to evaluate : 3.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 269 optimal weight: 9.9990 chunk 220 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 323 optimal weight: 7.9990 chunk 349 optimal weight: 6.9990 chunk 288 optimal weight: 10.0000 chunk 321 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 259 optimal weight: 0.9980 overall best weight: 3.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN C 77 HIS D 22 GLN ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 97 HIS ** J 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 185 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.6209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 31132 Z= 0.356 Angle : 0.741 8.521 42181 Z= 0.382 Chirality : 0.043 0.328 4756 Planarity : 0.005 0.076 5084 Dihedral : 15.959 178.516 4907 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.46 % Favored : 97.51 % Rotamer: Outliers : 0.45 % Allowed : 3.64 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.14), residues: 3570 helix: 0.80 (0.11), residues: 2076 sheet: 0.92 (0.26), residues: 354 loop : 0.35 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP G 211 HIS 0.011 0.002 HIS P 43 PHE 0.024 0.002 PHE L 196 TYR 0.029 0.002 TYR E 75 ARG 0.011 0.001 ARG J 231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 959 time to evaluate : 3.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.9446 (mt) cc_final: 0.9141 (mt) REVERT: A 131 GLU cc_start: 0.8501 (pp20) cc_final: 0.8263 (pp20) REVERT: A 159 ASP cc_start: 0.8292 (t70) cc_final: 0.7975 (t70) REVERT: A 162 GLU cc_start: 0.8993 (pp20) cc_final: 0.8776 (pp20) REVERT: A 247 ILE cc_start: 0.9023 (pt) cc_final: 0.8777 (pt) REVERT: B 97 HIS cc_start: 0.6967 (p-80) cc_final: 0.6679 (p-80) REVERT: B 210 MET cc_start: 0.7952 (mtt) cc_final: 0.7730 (mtm) REVERT: C 133 LEU cc_start: 0.9617 (mt) cc_final: 0.9388 (mm) REVERT: C 185 GLN cc_start: 0.7944 (mt0) cc_final: 0.7552 (mt0) REVERT: C 190 PHE cc_start: 0.8959 (m-80) cc_final: 0.8756 (m-80) REVERT: C 247 ILE cc_start: 0.8524 (mt) cc_final: 0.7429 (mt) REVERT: D 54 LYS cc_start: 0.9055 (tttt) cc_final: 0.8250 (ttmt) REVERT: E 42 LEU cc_start: 0.9184 (tp) cc_final: 0.8974 (tt) REVERT: E 46 LEU cc_start: 0.9271 (mt) cc_final: 0.8913 (mt) REVERT: E 104 ASP cc_start: 0.7450 (t70) cc_final: 0.6962 (t0) REVERT: E 107 LYS cc_start: 0.9062 (tttp) cc_final: 0.8601 (ttmm) REVERT: E 108 LYS cc_start: 0.9264 (mttm) cc_final: 0.8923 (mmmm) REVERT: E 119 LYS cc_start: 0.8518 (mmtt) cc_final: 0.7079 (mmtm) REVERT: E 190 PHE cc_start: 0.8922 (m-80) cc_final: 0.8562 (m-80) REVERT: F 103 LYS cc_start: 0.9247 (tttp) cc_final: 0.8820 (tptt) REVERT: F 125 PHE cc_start: 0.8529 (t80) cc_final: 0.8266 (t80) REVERT: F 144 ASP cc_start: 0.8531 (t70) cc_final: 0.8067 (t0) REVERT: F 145 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7724 (mt-10) REVERT: F 156 ASP cc_start: 0.8538 (m-30) cc_final: 0.8317 (m-30) REVERT: F 246 GLU cc_start: 0.7780 (pp20) cc_final: 0.7541 (tm-30) REVERT: G 176 LEU cc_start: 0.8873 (tp) cc_final: 0.8585 (tp) REVERT: G 190 PHE cc_start: 0.8697 (m-80) cc_final: 0.8367 (m-10) REVERT: G 229 MET cc_start: 0.2596 (mtt) cc_final: 0.2056 (mtt) REVERT: G 246 GLU cc_start: 0.7944 (pt0) cc_final: 0.7628 (pt0) REVERT: H 38 GLN cc_start: 0.8409 (tp40) cc_final: 0.7828 (tp40) REVERT: H 56 CYS cc_start: 0.7632 (m) cc_final: 0.6716 (m) REVERT: H 103 LYS cc_start: 0.9359 (tttt) cc_final: 0.9106 (pttt) REVERT: H 112 TYR cc_start: 0.8529 (t80) cc_final: 0.8307 (t80) REVERT: H 144 ASP cc_start: 0.8464 (t0) cc_final: 0.8210 (t0) REVERT: H 176 LEU cc_start: 0.9467 (tp) cc_final: 0.9204 (tt) REVERT: H 223 ASN cc_start: 0.8023 (t0) cc_final: 0.7601 (t0) REVERT: I 46 LEU cc_start: 0.9595 (mt) cc_final: 0.9356 (mt) REVERT: I 130 ILE cc_start: 0.9475 (pt) cc_final: 0.9070 (mm) REVERT: I 156 ASP cc_start: 0.7773 (m-30) cc_final: 0.7545 (m-30) REVERT: I 224 LEU cc_start: 0.8273 (mt) cc_final: 0.8023 (mt) REVERT: J 95 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7858 (mtp180) REVERT: J 185 GLN cc_start: 0.7903 (tp-100) cc_final: 0.7373 (tp40) REVERT: K 54 LYS cc_start: 0.8592 (tptp) cc_final: 0.8370 (tptp) REVERT: K 116 ARG cc_start: 0.7873 (mmp80) cc_final: 0.7345 (mmp80) REVERT: K 154 PHE cc_start: 0.9157 (m-80) cc_final: 0.8732 (m-80) REVERT: K 248 LEU cc_start: 0.8992 (mt) cc_final: 0.8647 (mt) REVERT: L 100 CYS cc_start: 0.6971 (t) cc_final: 0.6717 (t) REVERT: L 141 LEU cc_start: 0.8573 (tp) cc_final: 0.8107 (tp) REVERT: L 190 PHE cc_start: 0.7397 (m-10) cc_final: 0.7187 (m-10) REVERT: L 248 LEU cc_start: 0.8296 (pp) cc_final: 0.8027 (pp) REVERT: O 96 PRO cc_start: 0.8923 (Cg_exo) cc_final: 0.8621 (Cg_endo) REVERT: O 113 LEU cc_start: 0.8607 (tt) cc_final: 0.8331 (tt) REVERT: O 130 ILE cc_start: 0.9011 (pt) cc_final: 0.8794 (pt) REVERT: O 134 LYS cc_start: 0.8316 (ptpp) cc_final: 0.7790 (tptp) REVERT: P 106 PHE cc_start: 0.8680 (m-80) cc_final: 0.7968 (m-10) REVERT: P 113 LEU cc_start: 0.7953 (tt) cc_final: 0.7495 (tt) REVERT: P 130 ILE cc_start: 0.8982 (pt) cc_final: 0.8711 (pt) REVERT: P 263 ILE cc_start: 0.4328 (mp) cc_final: 0.4094 (mp) outliers start: 14 outliers final: 6 residues processed: 966 average time/residue: 0.4506 time to fit residues: 673.0744 Evaluate side-chains 698 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 692 time to evaluate : 3.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 8.9990 chunk 243 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 154 optimal weight: 0.0270 chunk 217 optimal weight: 6.9990 chunk 325 optimal weight: 10.0000 chunk 344 optimal weight: 0.9980 chunk 169 optimal weight: 8.9990 chunk 308 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 overall best weight: 1.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN D 97 HIS ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN H 185 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 185 GLN ** J 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 GLN ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.6609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31132 Z= 0.234 Angle : 0.673 10.346 42181 Z= 0.343 Chirality : 0.042 0.327 4756 Planarity : 0.004 0.058 5084 Dihedral : 15.616 173.142 4907 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.49 % Favored : 97.48 % Rotamer: Outliers : 0.16 % Allowed : 2.49 % Favored : 97.35 % 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: 1.05 (0.14), residues: 3570 helix: 0.99 (0.11), residues: 2012 sheet: 1.00 (0.26), residues: 358 loop : 0.32 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP P 211 HIS 0.011 0.001 HIS D 97 PHE 0.019 0.002 PHE G 190 TYR 0.019 0.002 TYR P 73 ARG 0.005 0.000 ARG F 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 933 time to evaluate : 3.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.9428 (mt) cc_final: 0.9089 (mt) REVERT: A 131 GLU cc_start: 0.8463 (pp20) cc_final: 0.8164 (pp20) REVERT: A 159 ASP cc_start: 0.8256 (t70) cc_final: 0.7919 (t70) REVERT: A 162 GLU cc_start: 0.8949 (pp20) cc_final: 0.8715 (pp20) REVERT: C 46 LEU cc_start: 0.9487 (mt) cc_final: 0.9280 (mt) REVERT: C 156 ASP cc_start: 0.8538 (m-30) cc_final: 0.8153 (m-30) REVERT: C 215 VAL cc_start: 0.8105 (t) cc_final: 0.7717 (t) REVERT: C 241 ILE cc_start: 0.8445 (tp) cc_final: 0.8179 (tp) REVERT: C 247 ILE cc_start: 0.8583 (mt) cc_final: 0.7498 (mt) REVERT: D 159 ASP cc_start: 0.8057 (m-30) cc_final: 0.7807 (m-30) REVERT: D 180 ILE cc_start: 0.9074 (mt) cc_final: 0.8754 (mt) REVERT: E 42 LEU cc_start: 0.9175 (tp) cc_final: 0.8958 (tt) REVERT: E 46 LEU cc_start: 0.9357 (mt) cc_final: 0.9010 (mt) REVERT: E 104 ASP cc_start: 0.7372 (t70) cc_final: 0.6963 (t0) REVERT: E 107 LYS cc_start: 0.9075 (tttp) cc_final: 0.8501 (ttmm) REVERT: E 108 LYS cc_start: 0.9243 (mttm) cc_final: 0.8836 (mmmm) REVERT: E 190 PHE cc_start: 0.8912 (m-80) cc_final: 0.8561 (m-80) REVERT: E 275 TYR cc_start: 0.5075 (m-10) cc_final: 0.4850 (m-10) REVERT: F 103 LYS cc_start: 0.9197 (tttp) cc_final: 0.8741 (tptt) REVERT: F 144 ASP cc_start: 0.8471 (t70) cc_final: 0.8044 (t0) REVERT: F 145 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7833 (mt-10) REVERT: F 156 ASP cc_start: 0.8543 (m-30) cc_final: 0.8231 (m-30) REVERT: G 176 LEU cc_start: 0.8766 (tp) cc_final: 0.8555 (tp) REVERT: G 190 PHE cc_start: 0.8702 (m-80) cc_final: 0.8492 (m-10) REVERT: G 229 MET cc_start: 0.2517 (mtt) cc_final: 0.2130 (mtt) REVERT: G 246 GLU cc_start: 0.7741 (pt0) cc_final: 0.7428 (pt0) REVERT: H 103 LYS cc_start: 0.9296 (tttt) cc_final: 0.9067 (pttt) REVERT: H 176 LEU cc_start: 0.9419 (tp) cc_final: 0.9170 (tt) REVERT: H 183 ASP cc_start: 0.7455 (t70) cc_final: 0.7248 (t70) REVERT: H 223 ASN cc_start: 0.7922 (t0) cc_final: 0.7548 (t0) REVERT: I 176 LEU cc_start: 0.9452 (tp) cc_final: 0.8986 (tp) REVERT: I 224 LEU cc_start: 0.8181 (mt) cc_final: 0.7936 (mt) REVERT: K 116 ARG cc_start: 0.7844 (mmp80) cc_final: 0.7633 (mmp80) REVERT: K 154 PHE cc_start: 0.9147 (m-80) cc_final: 0.8899 (m-80) REVERT: K 246 GLU cc_start: 0.7956 (pp20) cc_final: 0.7333 (pp20) REVERT: L 100 CYS cc_start: 0.7012 (t) cc_final: 0.6797 (t) REVERT: L 141 LEU cc_start: 0.8720 (tp) cc_final: 0.8183 (tp) REVERT: L 248 LEU cc_start: 0.8327 (pp) cc_final: 0.8019 (pp) REVERT: O 113 LEU cc_start: 0.8767 (tt) cc_final: 0.8529 (tp) REVERT: O 134 LYS cc_start: 0.8250 (ptpp) cc_final: 0.7874 (tptp) REVERT: P 106 PHE cc_start: 0.8665 (m-10) cc_final: 0.8087 (m-10) REVERT: P 113 LEU cc_start: 0.7511 (tt) cc_final: 0.6908 (tt) REVERT: P 130 ILE cc_start: 0.8957 (pt) cc_final: 0.8671 (pt) REVERT: P 263 ILE cc_start: 0.4541 (mp) cc_final: 0.4279 (mp) outliers start: 5 outliers final: 1 residues processed: 937 average time/residue: 0.4409 time to fit residues: 641.0934 Evaluate side-chains 696 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 695 time to evaluate : 3.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 5.9990 chunk 195 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 256 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 293 optimal weight: 8.9990 chunk 237 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 chunk 308 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 HIS ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 HIS ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN P 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.7039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 31132 Z= 0.322 Angle : 0.697 8.909 42181 Z= 0.358 Chirality : 0.043 0.357 4756 Planarity : 0.004 0.061 5084 Dihedral : 15.483 166.423 4907 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.55 % Favored : 97.42 % Rotamer: Outliers : 0.06 % Allowed : 2.24 % Favored : 97.70 % 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: 1.00 (0.14), residues: 3570 helix: 0.96 (0.12), residues: 2028 sheet: 0.93 (0.26), residues: 358 loop : 0.28 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP P 211 HIS 0.015 0.002 HIS B 97 PHE 0.019 0.002 PHE G 196 TYR 0.044 0.002 TYR K 240 ARG 0.010 0.001 ARG I 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 883 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8491 (pp20) cc_final: 0.8205 (pp20) REVERT: A 159 ASP cc_start: 0.8476 (t70) cc_final: 0.8060 (t70) REVERT: C 156 ASP cc_start: 0.8493 (m-30) cc_final: 0.8030 (m-30) REVERT: C 158 ARG cc_start: 0.8385 (tmm-80) cc_final: 0.6733 (ptm-80) REVERT: C 190 PHE cc_start: 0.8940 (m-80) cc_final: 0.8664 (m-10) REVERT: C 247 ILE cc_start: 0.8687 (mt) cc_final: 0.7599 (mt) REVERT: C 274 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6762 (pm20) REVERT: D 176 LEU cc_start: 0.9280 (tp) cc_final: 0.9011 (tp) REVERT: D 180 ILE cc_start: 0.9111 (mt) cc_final: 0.8788 (mt) REVERT: D 247 ILE cc_start: 0.8673 (mm) cc_final: 0.8131 (mm) REVERT: E 42 LEU cc_start: 0.9163 (tp) cc_final: 0.8934 (tt) REVERT: E 46 LEU cc_start: 0.9346 (mt) cc_final: 0.9023 (mt) REVERT: E 104 ASP cc_start: 0.7430 (t70) cc_final: 0.6963 (t0) REVERT: E 107 LYS cc_start: 0.9127 (tttp) cc_final: 0.8615 (ttmm) REVERT: E 108 LYS cc_start: 0.9302 (mttm) cc_final: 0.8978 (mmmm) REVERT: E 140 MET cc_start: 0.8140 (tpp) cc_final: 0.7855 (tpp) REVERT: E 190 PHE cc_start: 0.8949 (m-80) cc_final: 0.8574 (m-80) REVERT: F 144 ASP cc_start: 0.8642 (t70) cc_final: 0.8068 (t0) REVERT: F 145 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7892 (mt-10) REVERT: F 156 ASP cc_start: 0.8512 (m-30) cc_final: 0.8281 (m-30) REVERT: G 176 LEU cc_start: 0.8885 (tp) cc_final: 0.8669 (tp) REVERT: G 229 MET cc_start: 0.3096 (mtt) cc_final: 0.2675 (mtt) REVERT: H 103 LYS cc_start: 0.9343 (tttt) cc_final: 0.9129 (pttt) REVERT: H 144 ASP cc_start: 0.8827 (t0) cc_final: 0.8516 (t0) REVERT: H 183 ASP cc_start: 0.7650 (t70) cc_final: 0.7430 (t70) REVERT: I 130 ILE cc_start: 0.9513 (pt) cc_final: 0.9183 (mm) REVERT: I 156 ASP cc_start: 0.8706 (m-30) cc_final: 0.8458 (m-30) REVERT: I 224 LEU cc_start: 0.8194 (mt) cc_final: 0.7956 (mt) REVERT: J 180 ILE cc_start: 0.9158 (mt) cc_final: 0.8935 (mt) REVERT: K 246 GLU cc_start: 0.8014 (pp20) cc_final: 0.7361 (pp20) REVERT: K 253 ILE cc_start: 0.8346 (mm) cc_final: 0.8116 (mm) REVERT: L 100 CYS cc_start: 0.7062 (t) cc_final: 0.6790 (t) REVERT: L 141 LEU cc_start: 0.8746 (tp) cc_final: 0.8166 (tp) REVERT: L 248 LEU cc_start: 0.8423 (pp) cc_final: 0.8106 (pp) REVERT: O 117 VAL cc_start: 0.8815 (m) cc_final: 0.8591 (p) REVERT: O 134 LYS cc_start: 0.8308 (ptpp) cc_final: 0.7900 (tptp) REVERT: P 106 PHE cc_start: 0.8775 (m-10) cc_final: 0.8148 (m-10) REVERT: P 113 LEU cc_start: 0.7939 (tt) cc_final: 0.6850 (tt) REVERT: P 130 ILE cc_start: 0.9098 (pt) cc_final: 0.8829 (pt) REVERT: P 229 MET cc_start: 0.2412 (mtt) cc_final: 0.2171 (mtt) outliers start: 2 outliers final: 1 residues processed: 885 average time/residue: 0.4327 time to fit residues: 602.5789 Evaluate side-chains 658 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 656 time to evaluate : 4.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 2.9990 chunk 309 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 202 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 344 optimal weight: 0.1980 chunk 285 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 GLN ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.7217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31132 Z= 0.199 Angle : 0.675 13.943 42181 Z= 0.340 Chirality : 0.042 0.346 4756 Planarity : 0.004 0.050 5084 Dihedral : 15.266 163.803 4907 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.55 % Favored : 97.42 % Rotamer: Outliers : 0.06 % Allowed : 1.73 % Favored : 98.21 % 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: 1.05 (0.14), residues: 3570 helix: 1.01 (0.12), residues: 2030 sheet: 0.99 (0.26), residues: 358 loop : 0.27 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP G 211 HIS 0.010 0.001 HIS A 43 PHE 0.022 0.001 PHE G 190 TYR 0.025 0.002 TYR E 275 ARG 0.008 0.000 ARG D 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 893 time to evaluate : 3.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8479 (pp20) cc_final: 0.8146 (pp20) REVERT: A 159 ASP cc_start: 0.8319 (t70) cc_final: 0.8015 (t70) REVERT: B 111 GLU cc_start: 0.8078 (tp30) cc_final: 0.7870 (tp30) REVERT: C 156 ASP cc_start: 0.8360 (m-30) cc_final: 0.7853 (m-30) REVERT: C 162 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7662 (mt-10) REVERT: C 190 PHE cc_start: 0.8908 (m-80) cc_final: 0.8562 (m-10) REVERT: C 247 ILE cc_start: 0.8637 (mt) cc_final: 0.7710 (mt) REVERT: D 141 LEU cc_start: 0.9601 (tp) cc_final: 0.9387 (tt) REVERT: D 163 ASP cc_start: 0.8127 (m-30) cc_final: 0.7920 (m-30) REVERT: D 180 ILE cc_start: 0.9024 (mt) cc_final: 0.8727 (mt) REVERT: D 247 ILE cc_start: 0.8939 (mm) cc_final: 0.8333 (mm) REVERT: E 104 ASP cc_start: 0.7373 (t70) cc_final: 0.6991 (t0) REVERT: E 140 MET cc_start: 0.8156 (tpp) cc_final: 0.7836 (tpp) REVERT: F 144 ASP cc_start: 0.8541 (t70) cc_final: 0.8014 (t0) REVERT: F 156 ASP cc_start: 0.8470 (m-30) cc_final: 0.8238 (m-30) REVERT: G 159 ASP cc_start: 0.7781 (t70) cc_final: 0.7011 (t70) REVERT: G 176 LEU cc_start: 0.8749 (tp) cc_final: 0.8469 (tp) REVERT: G 180 ILE cc_start: 0.9200 (pt) cc_final: 0.8786 (pt) REVERT: G 229 MET cc_start: 0.3010 (mtt) cc_final: 0.2475 (mtt) REVERT: H 103 LYS cc_start: 0.9268 (tttt) cc_final: 0.9065 (pttt) REVERT: H 144 ASP cc_start: 0.8674 (t0) cc_final: 0.8367 (t0) REVERT: H 185 GLN cc_start: 0.8496 (mm110) cc_final: 0.8283 (mm110) REVERT: H 223 ASN cc_start: 0.7892 (t0) cc_final: 0.7528 (t0) REVERT: I 130 ILE cc_start: 0.9476 (pt) cc_final: 0.9170 (mm) REVERT: I 156 ASP cc_start: 0.8630 (m-30) cc_final: 0.8395 (m-30) REVERT: J 127 ASP cc_start: 0.8339 (m-30) cc_final: 0.7932 (m-30) REVERT: J 130 ILE cc_start: 0.9677 (pt) cc_final: 0.9120 (pt) REVERT: J 159 ASP cc_start: 0.7540 (t70) cc_final: 0.7333 (t0) REVERT: L 100 CYS cc_start: 0.6964 (t) cc_final: 0.6641 (t) REVERT: L 141 LEU cc_start: 0.8679 (tp) cc_final: 0.8133 (tp) REVERT: L 248 LEU cc_start: 0.8397 (pp) cc_final: 0.8093 (pp) REVERT: O 117 VAL cc_start: 0.8750 (m) cc_final: 0.8156 (p) REVERT: P 106 PHE cc_start: 0.8750 (m-10) cc_final: 0.8222 (m-10) REVERT: P 113 LEU cc_start: 0.7645 (tt) cc_final: 0.7065 (tt) REVERT: P 130 ILE cc_start: 0.8871 (pt) cc_final: 0.8561 (pt) REVERT: P 229 MET cc_start: 0.2450 (mtt) cc_final: 0.2177 (mtt) outliers start: 2 outliers final: 1 residues processed: 894 average time/residue: 0.4329 time to fit residues: 606.1223 Evaluate side-chains 667 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 666 time to evaluate : 3.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 251 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 289 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 343 optimal weight: 10.0000 chunk 214 optimal weight: 0.3980 chunk 209 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 GLN ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.7441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31132 Z= 0.229 Angle : 0.677 11.835 42181 Z= 0.344 Chirality : 0.042 0.390 4756 Planarity : 0.004 0.068 5084 Dihedral : 15.142 165.766 4907 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.55 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: 1.02 (0.14), residues: 3570 helix: 0.99 (0.12), residues: 2030 sheet: 0.99 (0.26), residues: 358 loop : 0.24 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP G 211 HIS 0.009 0.001 HIS A 43 PHE 0.022 0.001 PHE G 190 TYR 0.028 0.002 TYR G 93 ARG 0.012 0.000 ARG L 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 849 time to evaluate : 3.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8694 (m-30) cc_final: 0.8191 (m-30) REVERT: A 131 GLU cc_start: 0.8523 (pp20) cc_final: 0.8210 (pp20) REVERT: A 159 ASP cc_start: 0.8411 (t70) cc_final: 0.8021 (t70) REVERT: C 156 ASP cc_start: 0.8268 (m-30) cc_final: 0.7907 (m-30) REVERT: C 173 THR cc_start: 0.8199 (p) cc_final: 0.7969 (p) REVERT: D 141 LEU cc_start: 0.9570 (tp) cc_final: 0.9307 (tt) REVERT: D 159 ASP cc_start: 0.8074 (m-30) cc_final: 0.7770 (m-30) REVERT: D 176 LEU cc_start: 0.9169 (tp) cc_final: 0.8834 (tp) REVERT: D 180 ILE cc_start: 0.9085 (mt) cc_final: 0.8727 (mt) REVERT: D 184 GLU cc_start: 0.8324 (pm20) cc_final: 0.8056 (pm20) REVERT: E 104 ASP cc_start: 0.7386 (t70) cc_final: 0.7059 (t0) REVERT: E 140 MET cc_start: 0.8201 (tpp) cc_final: 0.7813 (tpp) REVERT: E 190 PHE cc_start: 0.8980 (m-80) cc_final: 0.8614 (m-80) REVERT: E 275 TYR cc_start: 0.5106 (m-10) cc_final: 0.4864 (m-80) REVERT: F 144 ASP cc_start: 0.8506 (t70) cc_final: 0.7917 (t0) REVERT: F 145 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8156 (mt-10) REVERT: G 115 TYR cc_start: 0.8123 (m-80) cc_final: 0.7417 (m-80) REVERT: G 176 LEU cc_start: 0.8799 (tp) cc_final: 0.8583 (tp) REVERT: G 229 MET cc_start: 0.3117 (mtt) cc_final: 0.2747 (mtt) REVERT: H 144 ASP cc_start: 0.8638 (t0) cc_final: 0.8331 (t0) REVERT: I 93 TYR cc_start: 0.9056 (t80) cc_final: 0.8809 (t80) REVERT: I 156 ASP cc_start: 0.8624 (m-30) cc_final: 0.8318 (m-30) REVERT: I 224 LEU cc_start: 0.8228 (mt) cc_final: 0.8012 (mt) REVERT: I 233 LEU cc_start: 0.8522 (mm) cc_final: 0.8289 (mm) REVERT: J 81 GLN cc_start: 0.7173 (pp30) cc_final: 0.6907 (pp30) REVERT: J 127 ASP cc_start: 0.8296 (m-30) cc_final: 0.7867 (m-30) REVERT: J 130 ILE cc_start: 0.9732 (pt) cc_final: 0.9165 (pt) REVERT: K 246 GLU cc_start: 0.8109 (pp20) cc_final: 0.7423 (pp20) REVERT: L 141 LEU cc_start: 0.8699 (tp) cc_final: 0.8196 (tp) REVERT: L 248 LEU cc_start: 0.8376 (pp) cc_final: 0.8008 (pp) REVERT: O 134 LYS cc_start: 0.7782 (tmtt) cc_final: 0.7507 (tptp) REVERT: P 105 LEU cc_start: 0.9084 (mt) cc_final: 0.8831 (pp) REVERT: P 113 LEU cc_start: 0.7440 (tt) cc_final: 0.6683 (tt) REVERT: P 185 GLN cc_start: 0.8152 (tt0) cc_final: 0.7928 (tt0) REVERT: P 229 MET cc_start: 0.2544 (mtt) cc_final: 0.2226 (mtt) outliers start: 0 outliers final: 0 residues processed: 849 average time/residue: 0.4572 time to fit residues: 603.3164 Evaluate side-chains 645 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 645 time to evaluate : 3.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 233 optimal weight: 0.9980 chunk 169 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 269 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 GLN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN P 97 HIS P 185 GLN ** P 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.7649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31132 Z= 0.234 Angle : 0.684 14.330 42181 Z= 0.348 Chirality : 0.043 0.427 4756 Planarity : 0.004 0.056 5084 Dihedral : 15.027 171.574 4907 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.63 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.14), residues: 3570 helix: 0.96 (0.12), residues: 2020 sheet: 0.99 (0.26), residues: 358 loop : 0.17 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP G 211 HIS 0.009 0.001 HIS A 43 PHE 0.021 0.001 PHE G 190 TYR 0.020 0.001 TYR B 112 ARG 0.017 0.001 ARG P 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 840 time to evaluate : 3.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8654 (m-30) cc_final: 0.8325 (m-30) REVERT: A 131 GLU cc_start: 0.8461 (pp20) cc_final: 0.8121 (pp20) REVERT: A 159 ASP cc_start: 0.8395 (t70) cc_final: 0.7976 (t70) REVERT: A 247 ILE cc_start: 0.9043 (pt) cc_final: 0.8826 (pt) REVERT: B 215 VAL cc_start: 0.7734 (t) cc_final: 0.6404 (t) REVERT: C 156 ASP cc_start: 0.8326 (m-30) cc_final: 0.7890 (m-30) REVERT: C 173 THR cc_start: 0.8018 (p) cc_final: 0.7809 (p) REVERT: D 141 LEU cc_start: 0.9594 (tp) cc_final: 0.9082 (tp) REVERT: D 159 ASP cc_start: 0.8001 (m-30) cc_final: 0.7666 (m-30) REVERT: D 176 LEU cc_start: 0.9159 (tp) cc_final: 0.8931 (tp) REVERT: D 180 ILE cc_start: 0.9018 (mt) cc_final: 0.8698 (mt) REVERT: D 184 GLU cc_start: 0.8327 (pm20) cc_final: 0.8049 (pm20) REVERT: E 104 ASP cc_start: 0.7376 (t70) cc_final: 0.7090 (t0) REVERT: E 140 MET cc_start: 0.8119 (tpp) cc_final: 0.7759 (tpp) REVERT: E 190 PHE cc_start: 0.9038 (m-80) cc_final: 0.8422 (m-80) REVERT: F 144 ASP cc_start: 0.8523 (t70) cc_final: 0.7882 (t0) REVERT: F 145 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8157 (mt-10) REVERT: G 159 ASP cc_start: 0.7451 (t70) cc_final: 0.7233 (t70) REVERT: G 174 ASP cc_start: 0.6766 (p0) cc_final: 0.6268 (p0) REVERT: G 176 LEU cc_start: 0.8802 (tp) cc_final: 0.8568 (tp) REVERT: G 229 MET cc_start: 0.2505 (mtt) cc_final: 0.1806 (mtt) REVERT: H 185 GLN cc_start: 0.8551 (mm110) cc_final: 0.8183 (mm110) REVERT: H 223 ASN cc_start: 0.8075 (t0) cc_final: 0.7810 (t0) REVERT: I 156 ASP cc_start: 0.8635 (m-30) cc_final: 0.8340 (m-30) REVERT: I 179 VAL cc_start: 0.9322 (t) cc_final: 0.8774 (t) REVERT: J 81 GLN cc_start: 0.7373 (pp30) cc_final: 0.7045 (pp30) REVERT: J 131 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7738 (mm-30) REVERT: K 246 GLU cc_start: 0.8289 (pp20) cc_final: 0.7446 (pp20) REVERT: L 141 LEU cc_start: 0.8732 (tp) cc_final: 0.8345 (tp) REVERT: L 248 LEU cc_start: 0.8349 (pp) cc_final: 0.8040 (pp) REVERT: O 134 LYS cc_start: 0.7719 (tmtt) cc_final: 0.7495 (tptp) REVERT: P 106 PHE cc_start: 0.8222 (m-80) cc_final: 0.7378 (m-80) REVERT: P 113 LEU cc_start: 0.7439 (tt) cc_final: 0.6716 (tt) REVERT: P 229 MET cc_start: 0.2595 (mtt) cc_final: 0.2328 (mtt) outliers start: 0 outliers final: 0 residues processed: 840 average time/residue: 0.3570 time to fit residues: 473.9830 Evaluate side-chains 642 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 642 time to evaluate : 4.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 7.9990 chunk 328 optimal weight: 8.9990 chunk 299 optimal weight: 5.9990 chunk 319 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 251 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 288 optimal weight: 0.8980 chunk 302 optimal weight: 6.9990 chunk 318 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN C 77 HIS ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 GLN L 77 HIS ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 HIS P 185 GLN ** P 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.8067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 31132 Z= 0.424 Angle : 0.792 11.095 42181 Z= 0.411 Chirality : 0.045 0.424 4756 Planarity : 0.005 0.071 5084 Dihedral : 15.194 177.730 4907 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.78 % Rotamer: Outliers : 0.03 % Allowed : 0.99 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.14), residues: 3570 helix: 0.59 (0.11), residues: 2094 sheet: 0.76 (0.26), residues: 360 loop : 0.08 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP G 211 HIS 0.008 0.002 HIS A 43 PHE 0.030 0.003 PHE G 190 TYR 0.025 0.002 TYR B 112 ARG 0.016 0.001 ARG O 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 780 time to evaluate : 3.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8651 (m-30) cc_final: 0.8276 (m-30) REVERT: A 131 GLU cc_start: 0.8533 (pp20) cc_final: 0.8195 (pp20) REVERT: A 159 ASP cc_start: 0.8550 (t70) cc_final: 0.8070 (t70) REVERT: C 127 ASP cc_start: 0.8686 (p0) cc_final: 0.8436 (p0) REVERT: C 156 ASP cc_start: 0.8323 (m-30) cc_final: 0.7880 (m-30) REVERT: D 176 LEU cc_start: 0.9223 (tp) cc_final: 0.8899 (tp) REVERT: D 180 ILE cc_start: 0.9136 (mt) cc_final: 0.8782 (mt) REVERT: D 184 GLU cc_start: 0.8560 (pm20) cc_final: 0.8326 (pm20) REVERT: E 104 ASP cc_start: 0.7371 (t70) cc_final: 0.7124 (t0) REVERT: E 140 MET cc_start: 0.8232 (tpp) cc_final: 0.7939 (tpp) REVERT: F 144 ASP cc_start: 0.8654 (t70) cc_final: 0.7938 (t0) REVERT: F 145 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8006 (mt-10) REVERT: G 174 ASP cc_start: 0.7006 (p0) cc_final: 0.6431 (p0) REVERT: H 112 TYR cc_start: 0.8328 (t80) cc_final: 0.8117 (t80) REVERT: H 144 ASP cc_start: 0.8693 (t0) cc_final: 0.8471 (t0) REVERT: H 156 ASP cc_start: 0.8902 (m-30) cc_final: 0.8645 (m-30) REVERT: H 185 GLN cc_start: 0.8639 (mm110) cc_final: 0.8271 (mm110) REVERT: H 223 ASN cc_start: 0.8047 (t0) cc_final: 0.7824 (t0) REVERT: H 229 MET cc_start: 0.8586 (pmm) cc_final: 0.8165 (pmm) REVERT: I 156 ASP cc_start: 0.8627 (m-30) cc_final: 0.8250 (m-30) REVERT: I 176 LEU cc_start: 0.9514 (tp) cc_final: 0.9308 (tp) REVERT: J 81 GLN cc_start: 0.7533 (pp30) cc_final: 0.7147 (pp30) REVERT: K 248 LEU cc_start: 0.9076 (mt) cc_final: 0.8864 (mt) REVERT: K 253 ILE cc_start: 0.8175 (mm) cc_final: 0.7950 (mm) REVERT: L 248 LEU cc_start: 0.8487 (pp) cc_final: 0.8241 (pp) REVERT: O 106 PHE cc_start: 0.8573 (m-80) cc_final: 0.8320 (m-80) REVERT: O 107 LYS cc_start: 0.8758 (tttm) cc_final: 0.8469 (tttm) REVERT: P 113 LEU cc_start: 0.7767 (tt) cc_final: 0.6855 (tt) REVERT: P 229 MET cc_start: 0.2832 (mtt) cc_final: 0.2524 (mtt) outliers start: 1 outliers final: 0 residues processed: 781 average time/residue: 0.4433 time to fit residues: 537.1500 Evaluate side-chains 598 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 598 time to evaluate : 3.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 0.8980 chunk 338 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 235 optimal weight: 0.5980 chunk 354 optimal weight: 20.0000 chunk 326 optimal weight: 0.9990 chunk 282 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 218 optimal weight: 0.9980 chunk 173 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 HIS ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 HIS P 97 HIS P 185 GLN ** P 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.8180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31132 Z= 0.243 Angle : 0.723 12.186 42181 Z= 0.369 Chirality : 0.045 0.423 4756 Planarity : 0.004 0.088 5084 Dihedral : 14.997 173.379 4907 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.89 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.14), residues: 3570 helix: 0.67 (0.11), residues: 2106 sheet: 0.89 (0.26), residues: 360 loop : 0.22 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP P 211 HIS 0.009 0.001 HIS A 43 PHE 0.032 0.002 PHE G 190 TYR 0.036 0.002 TYR F 73 ARG 0.013 0.001 ARG E 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 821 time to evaluate : 3.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8675 (m-30) cc_final: 0.8248 (m-30) REVERT: A 131 GLU cc_start: 0.8461 (pp20) cc_final: 0.8108 (pp20) REVERT: A 159 ASP cc_start: 0.8581 (t70) cc_final: 0.7597 (t70) REVERT: B 159 ASP cc_start: 0.7736 (m-30) cc_final: 0.7483 (m-30) REVERT: C 133 LEU cc_start: 0.9461 (mm) cc_final: 0.9252 (mm) REVERT: C 156 ASP cc_start: 0.8295 (m-30) cc_final: 0.7901 (m-30) REVERT: C 173 THR cc_start: 0.7878 (p) cc_final: 0.7597 (p) REVERT: D 141 LEU cc_start: 0.9547 (tp) cc_final: 0.9056 (tt) REVERT: D 176 LEU cc_start: 0.9185 (tp) cc_final: 0.8971 (tp) REVERT: D 180 ILE cc_start: 0.9080 (mt) cc_final: 0.8777 (mt) REVERT: D 184 GLU cc_start: 0.8320 (pm20) cc_final: 0.7996 (pm20) REVERT: D 190 PHE cc_start: 0.9361 (m-10) cc_final: 0.9114 (m-10) REVERT: D 246 GLU cc_start: 0.7675 (pp20) cc_final: 0.7045 (pp20) REVERT: E 97 HIS cc_start: 0.6943 (m170) cc_final: 0.6665 (m170) REVERT: E 140 MET cc_start: 0.8107 (tpp) cc_final: 0.7872 (tpp) REVERT: F 144 ASP cc_start: 0.8591 (t70) cc_final: 0.7915 (t0) REVERT: F 145 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8186 (mt-10) REVERT: G 159 ASP cc_start: 0.7502 (t70) cc_final: 0.7100 (t70) REVERT: G 174 ASP cc_start: 0.6844 (p0) cc_final: 0.6618 (p0) REVERT: H 156 ASP cc_start: 0.8911 (m-30) cc_final: 0.8707 (m-30) REVERT: H 176 LEU cc_start: 0.9528 (tt) cc_final: 0.9296 (tt) REVERT: H 185 GLN cc_start: 0.8577 (mm110) cc_final: 0.8189 (mm110) REVERT: H 223 ASN cc_start: 0.7937 (t0) cc_final: 0.7734 (t0) REVERT: H 229 MET cc_start: 0.8566 (pmm) cc_final: 0.8282 (pmm) REVERT: I 156 ASP cc_start: 0.8524 (m-30) cc_final: 0.8150 (m-30) REVERT: I 233 LEU cc_start: 0.8565 (mm) cc_final: 0.8255 (mm) REVERT: J 81 GLN cc_start: 0.7675 (pp30) cc_final: 0.7239 (pp30) REVERT: K 210 MET cc_start: 0.7358 (ptp) cc_final: 0.6207 (ptp) REVERT: K 246 GLU cc_start: 0.8272 (pp20) cc_final: 0.7381 (pp20) REVERT: K 248 LEU cc_start: 0.8962 (mt) cc_final: 0.8659 (mt) REVERT: L 141 LEU cc_start: 0.8809 (tp) cc_final: 0.8350 (tp) REVERT: L 248 LEU cc_start: 0.8576 (pp) cc_final: 0.8348 (pp) REVERT: P 106 PHE cc_start: 0.8274 (m-80) cc_final: 0.7758 (m-80) REVERT: P 113 LEU cc_start: 0.7838 (tt) cc_final: 0.7210 (tt) REVERT: P 229 MET cc_start: 0.2843 (mtt) cc_final: 0.2577 (mtt) outliers start: 0 outliers final: 0 residues processed: 821 average time/residue: 0.4695 time to fit residues: 604.7761 Evaluate side-chains 629 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 629 time to evaluate : 3.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 0.9980 chunk 300 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 260 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 282 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 chunk 290 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: