Starting phenix.real_space_refine on Mon Mar 11 07:01:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1u_32950/03_2024/7x1u_32950_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1u_32950/03_2024/7x1u_32950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1u_32950/03_2024/7x1u_32950.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1u_32950/03_2024/7x1u_32950.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1u_32950/03_2024/7x1u_32950_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1u_32950/03_2024/7x1u_32950_updated.pdb" } resolution = 3.19 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= 0.001 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 4782 2.51 5 N 1276 2.21 5 O 1384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 42": "OE1" <-> "OE2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 114": "OD1" <-> "OD2" Residue "B ASP 124": "OD1" <-> "OD2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B ASP 230": "OD1" <-> "OD2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 291": "OD1" <-> "OD2" Residue "C ASP 298": "OD1" <-> "OD2" Residue "C ASP 312": "OD1" <-> "OD2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "D TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 189": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7483 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 302 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 44} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 1918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1918 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 1 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 352 Unresolved non-hydrogen dihedrals: 246 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 150 Chain: "B" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1612 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 3 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 137 Chain: "C" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2269 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 5, 'TRANS': 324} Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 193 Chain: "D" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1356 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 10, 'TRANS': 197} Chain breaks: 7 Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 157 Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Unusual residues: {'NH2': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PCIS': 1, 'TRANS': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 4.97, per 1000 atoms: 0.66 Number of scatterers: 7483 At special positions: 0 Unit cell: (85.6, 113.42, 125.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1384 8.00 N 1276 7.00 C 4782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 179 " distance=2.03 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: 2.74 Conformation dependent library (CDL) restraints added in 1.5 seconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB PRO E 3 " Number of C-beta restraints generated: 2022 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 11 sheets defined 24.4% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'F' and resid 13 through 16 No H-bonds generated for 'chain 'F' and resid 13 through 16' Processing helix chain 'F' and resid 30 through 42 removed outlier: 4.132A pdb=" N MET F 38 " --> pdb=" O ALA F 34 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 removed outlier: 4.102A pdb=" N GLY A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 40 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 49 " --> pdb=" O MET A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 63 No H-bonds generated for 'chain 'A' and resid 60 through 63' Processing helix chain 'A' and resid 68 through 75 removed outlier: 4.083A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 removed outlier: 3.613A pdb=" N ASP A 85 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 103 through 112 removed outlier: 4.494A pdb=" N GLY A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE A 109 " --> pdb=" O GLN A 105 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN A 110 " --> pdb=" O TYR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 128 removed outlier: 3.695A pdb=" N ILE A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 135 No H-bonds generated for 'chain 'A' and resid 132 through 135' Processing helix chain 'A' and resid 139 through 162 removed outlier: 4.160A pdb=" N LYS A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LEU A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TRP A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE A 161 " --> pdb=" O CYS A 157 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE A 162 " --> pdb=" O MET A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 196 removed outlier: 3.743A pdb=" N MET A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASP A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 218 removed outlier: 3.741A pdb=" N ALA A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 208 " --> pdb=" O MET A 204 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 213 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILE A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.916A pdb=" N VAL A 271 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 removed outlier: 3.500A pdb=" N VAL A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 310 removed outlier: 4.679A pdb=" N ILE A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 322 removed outlier: 3.579A pdb=" N ASN A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Proline residue: A 317 - end of helix removed outlier: 3.539A pdb=" N TYR A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN A 321 " --> pdb=" O PRO A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 333 Processing helix chain 'B' and resid 16 through 19 No H-bonds generated for 'chain 'B' and resid 16 through 19' Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 125 through 129 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 150 through 153 No H-bonds generated for 'chain 'B' and resid 150 through 153' Processing helix chain 'B' and resid 160 through 163 No H-bonds generated for 'chain 'B' and resid 160 through 163' Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 184 through 201 removed outlier: 3.770A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 239 removed outlier: 4.259A pdb=" N ASP B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 25 removed outlier: 3.822A pdb=" N ILE C 18 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ARG C 19 " --> pdb=" O ASN C 16 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP C 20 " --> pdb=" O GLN C 17 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG C 22 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS C 23 " --> pdb=" O ASP C 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'A' and resid 167 through 171 removed outlier: 3.971A pdb=" N ASN A 167 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 178 " --> pdb=" O ASN A 167 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA A 174 " --> pdb=" O TYR A 171 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 212 through 215 removed outlier: 3.586A pdb=" N LEU B 143 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 110 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 109 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU B 38 " --> pdb=" O PHE B 84 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.740A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 111 through 113 Processing sheet with id= E, first strand: chain 'C' and resid 208 through 210 removed outlier: 3.525A pdb=" N SER C 201 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 262 through 264 removed outlier: 3.548A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 294 through 297 Processing sheet with id= H, first strand: chain 'C' and resid 327 through 329 removed outlier: 3.528A pdb=" N VAL C 327 " --> pdb=" O TRP C 339 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 166 through 170 removed outlier: 5.257A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 93 through 95 removed outlier: 3.975A pdb=" N TRP D 36 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 146 through 148 164 hydrogen bonds defined for protein. 456 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1227 1.31 - 1.43: 2053 1.43 - 1.56: 4284 1.56 - 1.69: 7 1.69 - 1.82: 53 Bond restraints: 7624 Sorted by residual: bond pdb=" C PCA E 1 " pdb=" N HIS E 2 " ideal model delta sigma weight residual 1.329 1.499 -0.170 1.40e-02 5.10e+03 1.47e+02 bond pdb=" C PRO E 3 " pdb=" N NH2 E 4 " ideal model delta sigma weight residual 1.329 1.476 -0.147 1.40e-02 5.10e+03 1.10e+02 bond pdb=" C HIS E 2 " pdb=" N PRO E 3 " ideal model delta sigma weight residual 1.341 1.507 -0.166 1.60e-02 3.91e+03 1.08e+02 bond pdb=" CA PRO E 3 " pdb=" CB PRO E 3 " ideal model delta sigma weight residual 1.530 1.352 0.178 2.00e-02 2.50e+03 7.95e+01 bond pdb=" CA PCA E 1 " pdb=" CB PCA E 1 " ideal model delta sigma weight residual 1.530 1.369 0.161 2.00e-02 2.50e+03 6.49e+01 ... (remaining 7619 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.94: 211 106.94 - 113.78: 4271 113.78 - 120.62: 3024 120.62 - 127.46: 2865 127.46 - 134.31: 76 Bond angle restraints: 10447 Sorted by residual: angle pdb=" N VAL A 49 " pdb=" CA VAL A 49 " pdb=" C VAL A 49 " ideal model delta sigma weight residual 111.90 107.34 4.56 8.10e-01 1.52e+00 3.16e+01 angle pdb=" N TYR A 181 " pdb=" CA TYR A 181 " pdb=" C TYR A 181 " ideal model delta sigma weight residual 108.23 115.97 -7.74 1.38e+00 5.25e-01 3.14e+01 angle pdb=" N VAL A 264 " pdb=" CA VAL A 264 " pdb=" C VAL A 264 " ideal model delta sigma weight residual 112.83 107.32 5.51 9.90e-01 1.02e+00 3.10e+01 angle pdb=" N ILE B 227 " pdb=" CA ILE B 227 " pdb=" C ILE B 227 " ideal model delta sigma weight residual 112.96 107.47 5.49 1.00e+00 1.00e+00 3.02e+01 angle pdb=" C ASP C 195 " pdb=" N THR C 196 " pdb=" CA THR C 196 " ideal model delta sigma weight residual 121.54 132.01 -10.47 1.91e+00 2.74e-01 3.00e+01 ... (remaining 10442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 3945 16.39 - 32.78: 386 32.78 - 49.17: 68 49.17 - 65.56: 4 65.56 - 81.95: 2 Dihedral angle restraints: 4405 sinusoidal: 1282 harmonic: 3123 Sorted by residual: dihedral pdb=" C HIS E 2 " pdb=" N HIS E 2 " pdb=" CA HIS E 2 " pdb=" CB HIS E 2 " ideal model delta harmonic sigma weight residual -122.60 -137.12 14.52 0 2.50e+00 1.60e-01 3.37e+01 dihedral pdb=" CA TYR D 223 " pdb=" C TYR D 223 " pdb=" N PRO D 224 " pdb=" CA PRO D 224 " ideal model delta harmonic sigma weight residual 180.00 -153.86 -26.14 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA PHE D 108 " pdb=" C PHE D 108 " pdb=" N ASP D 109 " pdb=" CA ASP D 109 " ideal model delta harmonic sigma weight residual 180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 4402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.076: 1283 1.076 - 2.151: 0 2.151 - 3.226: 0 3.226 - 4.302: 0 4.302 - 5.377: 1 Chirality restraints: 1284 Sorted by residual: chirality pdb=" CA PRO E 3 " pdb=" N PRO E 3 " pdb=" C PRO E 3 " pdb=" CB PRO E 3 " both_signs ideal model delta sigma weight residual False 2.72 -2.66 5.38 2.00e-01 2.50e+01 7.23e+02 chirality pdb=" CA HIS E 2 " pdb=" N HIS E 2 " pdb=" C HIS E 2 " pdb=" CB HIS E 2 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" CA PCA E 1 " pdb=" N PCA E 1 " pdb=" C PCA E 1 " pdb=" CB PCA E 1 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1281 not shown) Planarity restraints: 1332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 316 " 0.058 5.00e-02 4.00e+02 8.74e-02 1.22e+01 pdb=" N PRO A 317 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 317 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 317 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 187 " -0.057 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO D 188 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO D 188 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 188 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 223 " -0.052 5.00e-02 4.00e+02 7.70e-02 9.48e+00 pdb=" N PRO D 224 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO D 224 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 224 " -0.036 5.00e-02 4.00e+02 ... (remaining 1329 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 410 2.71 - 3.26: 7029 3.26 - 3.81: 12283 3.81 - 4.35: 14670 4.35 - 4.90: 24629 Nonbonded interactions: 59021 Sorted by model distance: nonbonded pdb=" NH2 ARG A 306 " pdb=" N NH2 E 4 " model vdw 2.166 2.560 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.190 2.440 nonbonded pdb=" NE ARG A 306 " pdb=" N NH2 E 4 " model vdw 2.273 2.560 nonbonded pdb=" OG SER C 227 " pdb=" OD1 ASP C 228 " model vdw 2.281 2.440 nonbonded pdb=" CZ ARG A 306 " pdb=" C PRO E 3 " model vdw 2.298 2.800 ... (remaining 59016 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.170 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.690 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 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 : 0.008 0.178 7624 Z= 0.548 Angle : 1.031 13.689 10447 Z= 0.575 Chirality : 0.161 5.377 1284 Planarity : 0.007 0.087 1332 Dihedral : 13.418 81.955 2380 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.74 % Favored : 92.17 % Rotamer: Outliers : 0.46 % Allowed : 10.09 % Favored : 89.45 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 3.03 % 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: -5.61 (0.19), residues: 1047 helix: -4.86 (0.12), residues: 294 sheet: -3.25 (0.31), residues: 214 loop : -3.23 (0.22), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 36 HIS 0.010 0.002 HIS B 82 PHE 0.024 0.003 PHE D 27 TYR 0.023 0.002 TYR C 59 ARG 0.004 0.001 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 174 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 49 ARG cc_start: 0.7806 (mpt90) cc_final: 0.7289 (mpp-170) REVERT: D 110 PHE cc_start: 0.7172 (t80) cc_final: 0.6694 (t80) outliers start: 3 outliers final: 2 residues processed: 177 average time/residue: 0.2074 time to fit residues: 48.3008 Evaluate side-chains 136 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain C residue 315 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 42 optimal weight: 0.0970 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 GLN B 98 GLN B 237 GLN C 62 HIS C 88 ASN C 225 HIS D 174 GLN D 220 HIS E 2 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7624 Z= 0.229 Angle : 0.682 16.315 10447 Z= 0.345 Chirality : 0.046 0.316 1284 Planarity : 0.006 0.072 1332 Dihedral : 6.459 28.438 1135 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.12 % Favored : 91.79 % Rotamer: Outliers : 3.21 % Allowed : 17.58 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -4.95 (0.21), residues: 1047 helix: -4.17 (0.16), residues: 304 sheet: -2.86 (0.32), residues: 219 loop : -2.86 (0.23), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 96 HIS 0.006 0.001 HIS C 225 PHE 0.023 0.002 PHE A 148 TYR 0.016 0.001 TYR D 50 ARG 0.010 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 144 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 123 ARG cc_start: 0.7819 (mtt180) cc_final: 0.7578 (mtt180) REVERT: A 310 TYR cc_start: 0.7691 (m-10) cc_final: 0.6762 (m-10) REVERT: A 318 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8626 (m) REVERT: B 25 GLU cc_start: 0.7718 (pt0) cc_final: 0.7379 (pt0) REVERT: B 232 LYS cc_start: 0.7826 (ttmt) cc_final: 0.7571 (tttm) REVERT: C 228 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7699 (p0) REVERT: C 323 ASP cc_start: 0.7695 (p0) cc_final: 0.6765 (p0) outliers start: 21 outliers final: 10 residues processed: 155 average time/residue: 0.1749 time to fit residues: 37.4314 Evaluate side-chains 142 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.0770 chunk 29 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 overall best weight: 1.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN B 82 HIS B 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7624 Z= 0.267 Angle : 0.686 17.376 10447 Z= 0.338 Chirality : 0.046 0.241 1284 Planarity : 0.005 0.062 1332 Dihedral : 6.156 28.996 1135 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.31 % Favored : 91.60 % Rotamer: Outliers : 4.28 % Allowed : 20.03 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -4.38 (0.22), residues: 1047 helix: -3.60 (0.19), residues: 304 sheet: -2.63 (0.32), residues: 235 loop : -2.49 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 47 HIS 0.006 0.001 HIS B 82 PHE 0.019 0.002 PHE A 148 TYR 0.016 0.001 TYR D 50 ARG 0.008 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 139 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 TYR cc_start: 0.7636 (m-10) cc_final: 0.6654 (m-10) REVERT: B 25 GLU cc_start: 0.7763 (pt0) cc_final: 0.7443 (pt0) REVERT: B 142 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.7120 (t80) REVERT: B 232 LYS cc_start: 0.7915 (ttmt) cc_final: 0.7610 (tttm) REVERT: C 49 ARG cc_start: 0.7863 (mpt90) cc_final: 0.7159 (mpp80) REVERT: C 228 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7803 (p0) REVERT: C 323 ASP cc_start: 0.7689 (p0) cc_final: 0.6744 (p0) outliers start: 28 outliers final: 19 residues processed: 156 average time/residue: 0.1607 time to fit residues: 35.3422 Evaluate side-chains 152 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 50 optimal weight: 0.0570 chunk 10 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 0.4980 chunk 102 optimal weight: 0.3980 chunk 91 optimal weight: 0.0670 chunk 27 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 7624 Z= 0.150 Angle : 0.613 16.662 10447 Z= 0.298 Chirality : 0.043 0.243 1284 Planarity : 0.004 0.057 1332 Dihedral : 5.433 28.102 1134 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.54 % Favored : 94.36 % Rotamer: Outliers : 2.75 % Allowed : 23.09 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -3.80 (0.23), residues: 1047 helix: -2.89 (0.23), residues: 298 sheet: -2.31 (0.33), residues: 230 loop : -2.31 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 47 HIS 0.003 0.001 HIS C 225 PHE 0.017 0.001 PHE A 148 TYR 0.018 0.001 TYR C 111 ARG 0.005 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 1.237 Fit side-chains revert: symmetry clash REVERT: A 166 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6368 (mm) REVERT: A 310 TYR cc_start: 0.7539 (m-10) cc_final: 0.6749 (m-10) REVERT: B 25 GLU cc_start: 0.7726 (pt0) cc_final: 0.7401 (pt0) REVERT: B 142 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6820 (t80) REVERT: B 232 LYS cc_start: 0.7763 (ttmt) cc_final: 0.7554 (tttm) REVERT: C 49 ARG cc_start: 0.7733 (mpt90) cc_final: 0.7292 (mpp-170) REVERT: C 234 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.6855 (t80) REVERT: C 323 ASP cc_start: 0.7525 (p0) cc_final: 0.6619 (p0) outliers start: 18 outliers final: 12 residues processed: 146 average time/residue: 0.1841 time to fit residues: 37.4946 Evaluate side-chains 141 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain D residue 80 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 0.0670 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 7624 Z= 0.373 Angle : 0.739 17.612 10447 Z= 0.360 Chirality : 0.048 0.235 1284 Planarity : 0.005 0.052 1332 Dihedral : 6.008 30.618 1134 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.17 % Favored : 90.74 % Rotamer: Outliers : 5.20 % Allowed : 22.32 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -3.77 (0.24), residues: 1047 helix: -2.83 (0.23), residues: 303 sheet: -2.39 (0.33), residues: 240 loop : -2.23 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D 47 HIS 0.007 0.001 HIS C 225 PHE 0.025 0.003 PHE A 148 TYR 0.021 0.002 TYR C 111 ARG 0.006 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 166 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6442 (mm) REVERT: A 310 TYR cc_start: 0.7675 (m-10) cc_final: 0.6654 (m-10) REVERT: B 25 GLU cc_start: 0.7753 (pt0) cc_final: 0.7476 (pt0) REVERT: C 49 ARG cc_start: 0.7926 (mpt90) cc_final: 0.7411 (mpp-170) REVERT: C 228 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7811 (p0) REVERT: C 323 ASP cc_start: 0.7728 (p0) cc_final: 0.6789 (p0) outliers start: 34 outliers final: 27 residues processed: 149 average time/residue: 0.1584 time to fit residues: 33.6960 Evaluate side-chains 150 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 25 optimal weight: 0.1980 chunk 102 optimal weight: 0.0170 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 98 optimal weight: 0.0770 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7624 Z= 0.147 Angle : 0.613 16.352 10447 Z= 0.296 Chirality : 0.043 0.228 1284 Planarity : 0.004 0.052 1332 Dihedral : 5.199 29.069 1134 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.25 % Favored : 94.65 % Rotamer: Outliers : 3.36 % Allowed : 25.23 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -3.34 (0.24), residues: 1047 helix: -2.26 (0.26), residues: 301 sheet: -2.26 (0.34), residues: 232 loop : -2.07 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 47 HIS 0.003 0.001 HIS B 209 PHE 0.022 0.001 PHE A 148 TYR 0.017 0.001 TYR D 102 ARG 0.007 0.001 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 166 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6408 (mm) REVERT: A 310 TYR cc_start: 0.7461 (m-10) cc_final: 0.6603 (m-10) REVERT: B 25 GLU cc_start: 0.7697 (pt0) cc_final: 0.7382 (pt0) REVERT: B 142 PHE cc_start: 0.7168 (OUTLIER) cc_final: 0.6709 (t80) REVERT: C 49 ARG cc_start: 0.7733 (mpt90) cc_final: 0.7202 (mpp-170) REVERT: C 234 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.6869 (t80) REVERT: C 323 ASP cc_start: 0.7547 (p0) cc_final: 0.6579 (p0) outliers start: 22 outliers final: 13 residues processed: 150 average time/residue: 0.1633 time to fit residues: 35.1018 Evaluate side-chains 139 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 0.0870 chunk 40 optimal weight: 5.9990 chunk 61 optimal weight: 0.0060 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7624 Z= 0.156 Angle : 0.618 16.148 10447 Z= 0.297 Chirality : 0.043 0.196 1284 Planarity : 0.004 0.050 1332 Dihedral : 5.041 29.487 1134 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.06 % Favored : 94.84 % Rotamer: Outliers : 4.13 % Allowed : 25.08 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -3.03 (0.24), residues: 1047 helix: -2.00 (0.27), residues: 292 sheet: -2.01 (0.35), residues: 227 loop : -1.94 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 47 HIS 0.004 0.001 HIS C 225 PHE 0.024 0.001 PHE A 148 TYR 0.008 0.001 TYR D 102 ARG 0.004 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 138 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6477 (mm) REVERT: A 310 TYR cc_start: 0.7406 (m-10) cc_final: 0.6598 (m-10) REVERT: B 25 GLU cc_start: 0.7677 (pt0) cc_final: 0.7367 (pt0) REVERT: B 142 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.6651 (t80) REVERT: C 49 ARG cc_start: 0.7683 (mpt90) cc_final: 0.7208 (mpp-170) REVERT: C 234 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6991 (t80) REVERT: C 323 ASP cc_start: 0.7440 (p0) cc_final: 0.6560 (p0) outliers start: 27 outliers final: 16 residues processed: 157 average time/residue: 0.1681 time to fit residues: 37.1424 Evaluate side-chains 146 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.0370 chunk 19 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 92 optimal weight: 0.0870 chunk 97 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7624 Z= 0.197 Angle : 0.631 16.287 10447 Z= 0.303 Chirality : 0.044 0.215 1284 Planarity : 0.004 0.051 1332 Dihedral : 5.107 30.623 1134 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.73 % Favored : 94.17 % Rotamer: Outliers : 3.98 % Allowed : 25.23 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.95 (0.25), residues: 1047 helix: -1.91 (0.27), residues: 294 sheet: -1.99 (0.35), residues: 229 loop : -1.89 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 47 HIS 0.005 0.001 HIS C 225 PHE 0.024 0.002 PHE A 148 TYR 0.014 0.001 TYR C 111 ARG 0.004 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: F 38 MET cc_start: 0.6580 (pmm) cc_final: 0.6336 (pmm) REVERT: A 166 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6457 (mm) REVERT: A 310 TYR cc_start: 0.7410 (m-10) cc_final: 0.6504 (m-10) REVERT: B 25 GLU cc_start: 0.7679 (pt0) cc_final: 0.7365 (pt0) REVERT: B 142 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6768 (t80) REVERT: C 49 ARG cc_start: 0.7751 (mpt90) cc_final: 0.7319 (mpp-170) REVERT: C 234 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.6982 (t80) REVERT: D 166 LEU cc_start: 0.3984 (mp) cc_final: 0.3773 (mp) outliers start: 26 outliers final: 20 residues processed: 144 average time/residue: 0.1607 time to fit residues: 33.0352 Evaluate side-chains 146 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.7980 chunk 97 optimal weight: 20.0000 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 0.0370 chunk 74 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 chunk 90 optimal weight: 0.3980 chunk 94 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7624 Z= 0.161 Angle : 0.610 16.036 10447 Z= 0.292 Chirality : 0.043 0.143 1284 Planarity : 0.004 0.052 1332 Dihedral : 4.888 29.778 1134 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.97 % Favored : 94.94 % Rotamer: Outliers : 4.13 % Allowed : 25.69 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.78 (0.25), residues: 1047 helix: -1.67 (0.28), residues: 294 sheet: -2.06 (0.33), residues: 239 loop : -1.74 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 47 HIS 0.004 0.001 HIS C 225 PHE 0.023 0.001 PHE A 148 TYR 0.011 0.001 TYR C 111 ARG 0.003 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: F 38 MET cc_start: 0.6778 (pmm) cc_final: 0.6506 (pmm) REVERT: A 166 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6549 (mm) REVERT: A 310 TYR cc_start: 0.7372 (m-10) cc_final: 0.6559 (m-10) REVERT: B 25 GLU cc_start: 0.7670 (pt0) cc_final: 0.7330 (pt0) REVERT: B 95 LYS cc_start: 0.7370 (mmmm) cc_final: 0.6980 (mmtm) REVERT: B 142 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.6597 (t80) REVERT: C 49 ARG cc_start: 0.7661 (mpt90) cc_final: 0.7167 (mpp-170) REVERT: C 234 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.7010 (t80) REVERT: C 323 ASP cc_start: 0.7355 (p0) cc_final: 0.6361 (p0) REVERT: D 166 LEU cc_start: 0.3878 (mp) cc_final: 0.3645 (mp) outliers start: 27 outliers final: 21 residues processed: 152 average time/residue: 0.1560 time to fit residues: 33.9637 Evaluate side-chains 153 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7624 Z= 0.329 Angle : 0.704 16.966 10447 Z= 0.342 Chirality : 0.047 0.168 1284 Planarity : 0.005 0.054 1332 Dihedral : 5.466 31.598 1134 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.64 % Favored : 92.26 % Rotamer: Outliers : 3.98 % Allowed : 26.15 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.86 (0.25), residues: 1047 helix: -1.85 (0.27), residues: 296 sheet: -1.98 (0.34), residues: 233 loop : -1.78 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP D 47 HIS 0.006 0.001 HIS C 225 PHE 0.025 0.002 PHE A 148 TYR 0.020 0.001 TYR D 50 ARG 0.005 0.000 ARG A 306 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: F 38 MET cc_start: 0.6825 (pmm) cc_final: 0.6518 (pmm) REVERT: A 166 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6467 (mm) REVERT: B 25 GLU cc_start: 0.7732 (pt0) cc_final: 0.7388 (pt0) REVERT: C 49 ARG cc_start: 0.7753 (mpt90) cc_final: 0.7231 (mpp-170) REVERT: C 323 ASP cc_start: 0.7470 (p0) cc_final: 0.6574 (p0) outliers start: 26 outliers final: 22 residues processed: 149 average time/residue: 0.1568 time to fit residues: 33.4002 Evaluate side-chains 149 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.0570 chunk 77 optimal weight: 0.0050 chunk 12 optimal weight: 0.0170 chunk 23 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 10 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 overall best weight: 0.3750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.198968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.164815 restraints weight = 10921.662| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 3.10 r_work: 0.4059 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7624 Z= 0.152 Angle : 0.618 15.717 10447 Z= 0.298 Chirality : 0.043 0.144 1284 Planarity : 0.004 0.052 1332 Dihedral : 4.887 29.212 1134 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.58 % Favored : 95.32 % Rotamer: Outliers : 3.67 % Allowed : 25.99 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.71 (0.25), residues: 1047 helix: -1.57 (0.28), residues: 305 sheet: -2.11 (0.33), residues: 242 loop : -1.66 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 47 HIS 0.004 0.001 HIS C 225 PHE 0.024 0.001 PHE A 148 TYR 0.012 0.001 TYR D 102 ARG 0.002 0.000 ARG A 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2032.13 seconds wall clock time: 37 minutes 22.02 seconds (2242.02 seconds total)