Starting phenix.real_space_refine on Mon Dec 11 09:41:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj3_0010/12_2023/6gj3_0010.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj3_0010/12_2023/6gj3_0010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj3_0010/12_2023/6gj3_0010.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj3_0010/12_2023/6gj3_0010.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj3_0010/12_2023/6gj3_0010.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj3_0010/12_2023/6gj3_0010.pdb" } resolution = 4.3 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= 1.000 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 80 5.16 5 C 11009 2.51 5 N 3160 2.21 5 O 3156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 218": "NH1" <-> "NH2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "D PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 259": "NH1" <-> "NH2" Residue "F PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 94": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 17405 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 479 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 7, 'TRANS': 54} Chain breaks: 1 Chain: "D" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2473 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 289} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 2479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2479 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 289} 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: "F" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2482 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 289} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3509 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 29, 'TRANS': 414} Chain: "H" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3498 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 29, 'TRANS': 414} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2485 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 21, 'TRANS': 289} Time building chain proxies: 9.21, per 1000 atoms: 0.53 Number of scatterers: 17405 At special positions: 0 Unit cell: (106.7, 159.5, 140.8, 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 80 16.00 O 3156 8.00 N 3160 7.00 C 11009 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=0, symmetry=0 Time building additional restraints: 6.50 Conformation dependent library (CDL) restraints added in 3.2 seconds 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4230 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 24 sheets defined 31.4% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'D' and resid 15 through 35 removed outlier: 3.972A pdb=" N PHE D 19 " --> pdb=" O MET D 15 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN D 21 " --> pdb=" O GLN D 17 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TRP D 25 " --> pdb=" O GLN D 21 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP D 26 " --> pdb=" O GLN D 22 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER D 32 " --> pdb=" O HIS D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 193 Processing helix chain 'D' and resid 194 through 218 removed outlier: 3.784A pdb=" N MET D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA D 210 " --> pdb=" O HIS D 206 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG D 211 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 245 removed outlier: 3.637A pdb=" N ALA D 242 " --> pdb=" O TRP D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 256 removed outlier: 3.908A pdb=" N LEU D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N MET D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 275 removed outlier: 4.372A pdb=" N LEU D 264 " --> pdb=" O HIS D 260 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 298 through 310 Processing helix chain 'E' and resid 15 through 33 removed outlier: 3.987A pdb=" N PHE E 19 " --> pdb=" O MET E 15 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN E 21 " --> pdb=" O GLN E 17 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN E 22 " --> pdb=" O GLN E 18 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP E 26 " --> pdb=" O GLN E 22 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL E 27 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA E 30 " --> pdb=" O ASP E 26 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP E 31 " --> pdb=" O VAL E 27 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER E 32 " --> pdb=" O HIS E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 193 Processing helix chain 'E' and resid 194 through 218 removed outlier: 4.424A pdb=" N MET E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR E 199 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN E 209 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 242 removed outlier: 3.611A pdb=" N LEU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 251 removed outlier: 3.547A pdb=" N LEU E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 277 removed outlier: 3.660A pdb=" N ARG E 266 " --> pdb=" O GLU E 262 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU E 267 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG E 270 " --> pdb=" O ARG E 266 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU E 271 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR E 277 " --> pdb=" O GLY E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 297 removed outlier: 3.713A pdb=" N ASN E 297 " --> pdb=" O THR E 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 294 through 297' Processing helix chain 'E' and resid 298 through 310 removed outlier: 3.573A pdb=" N ASN E 307 " --> pdb=" O LEU E 303 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG E 308 " --> pdb=" O SER E 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 35 removed outlier: 3.843A pdb=" N GLN F 20 " --> pdb=" O PRO F 16 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN F 21 " --> pdb=" O GLN F 17 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL F 27 " --> pdb=" O ALA F 23 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA F 34 " --> pdb=" O ALA F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 57 Processing helix chain 'F' and resid 194 through 222 removed outlier: 4.437A pdb=" N MET F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR F 199 " --> pdb=" O PRO F 195 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLU F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU F 204 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU F 215 " --> pdb=" O ARG F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 244 Processing helix chain 'F' and resid 246 through 251 removed outlier: 3.705A pdb=" N LEU F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 275 removed outlier: 3.545A pdb=" N GLU F 267 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU F 275 " --> pdb=" O LEU F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 297 Processing helix chain 'F' and resid 298 through 310 removed outlier: 3.582A pdb=" N ASN F 307 " --> pdb=" O LEU F 303 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG F 308 " --> pdb=" O SER F 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 36 removed outlier: 4.351A pdb=" N GLN G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA G 30 " --> pdb=" O ASP G 26 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N MET G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 218 removed outlier: 4.264A pdb=" N THR G 199 " --> pdb=" O PRO G 195 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 223 Processing helix chain 'G' and resid 230 through 245 removed outlier: 3.732A pdb=" N VAL G 234 " --> pdb=" O ALA G 230 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU G 236 " --> pdb=" O ALA G 232 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER G 245 " --> pdb=" O ASN G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 253 removed outlier: 3.630A pdb=" N LEU G 250 " --> pdb=" O ALA G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 276 removed outlier: 4.410A pdb=" N LEU G 264 " --> pdb=" O HIS G 260 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG G 266 " --> pdb=" O GLU G 262 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU G 267 " --> pdb=" O LEU G 263 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG G 270 " --> pdb=" O ARG G 266 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU G 271 " --> pdb=" O GLU G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 297 removed outlier: 3.503A pdb=" N ASN G 297 " --> pdb=" O THR G 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 294 through 297' Processing helix chain 'G' and resid 298 through 310 Processing helix chain 'G' and resid 354 through 366 removed outlier: 4.407A pdb=" N THR G 360 " --> pdb=" O HIS G 356 " (cutoff:3.500A) Proline residue: G 363 - end of helix Processing helix chain 'G' and resid 411 through 420 removed outlier: 3.735A pdb=" N ASP G 420 " --> pdb=" O ARG G 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 35 removed outlier: 4.331A pdb=" N PHE H 19 " --> pdb=" O MET H 15 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA H 34 " --> pdb=" O ALA H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 223 removed outlier: 4.105A pdb=" N MET H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG H 211 " --> pdb=" O HIS H 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG H 212 " --> pdb=" O LEU H 208 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN H 213 " --> pdb=" O GLN H 209 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG H 214 " --> pdb=" O ALA H 210 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN H 222 " --> pdb=" O MET H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 254 removed outlier: 4.037A pdb=" N SER H 245 " --> pdb=" O ASN H 241 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA H 246 " --> pdb=" O ALA H 242 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU H 247 " --> pdb=" O LEU H 243 " (cutoff:3.500A) Proline residue: H 248 - end of helix removed outlier: 5.335A pdb=" N GLU H 252 " --> pdb=" O PRO H 248 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU H 253 " --> pdb=" O VAL H 249 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU H 254 " --> pdb=" O LEU H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 260 through 275 removed outlier: 4.121A pdb=" N LEU H 264 " --> pdb=" O HIS H 260 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU H 267 " --> pdb=" O LEU H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 287 Processing helix chain 'H' and resid 298 through 310 removed outlier: 3.785A pdb=" N LEU H 302 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG H 308 " --> pdb=" O SER H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 341 removed outlier: 3.940A pdb=" N ARG H 340 " --> pdb=" O ALA H 337 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 422 removed outlier: 3.958A pdb=" N ARG H 416 " --> pdb=" O THR H 412 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 24 removed outlier: 4.277A pdb=" N PHE I 19 " --> pdb=" O MET I 15 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN I 20 " --> pdb=" O PRO I 16 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN I 21 " --> pdb=" O GLN I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 35 Processing helix chain 'I' and resid 51 through 56 removed outlier: 3.572A pdb=" N LEU I 54 " --> pdb=" O ASP I 51 " (cutoff:3.500A) Proline residue: I 55 - end of helix No H-bonds generated for 'chain 'I' and resid 51 through 56' Processing helix chain 'I' and resid 89 through 92 Processing helix chain 'I' and resid 194 through 220 removed outlier: 4.138A pdb=" N LEU I 202 " --> pdb=" O MET I 198 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU I 203 " --> pdb=" O THR I 199 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA I 210 " --> pdb=" O HIS I 206 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG I 211 " --> pdb=" O HIS I 207 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG I 219 " --> pdb=" O LEU I 215 " (cutoff:3.500A) Processing helix chain 'I' and resid 224 through 228 removed outlier: 3.740A pdb=" N ASP I 228 " --> pdb=" O ARG I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 245 removed outlier: 3.900A pdb=" N SER I 235 " --> pdb=" O VAL I 231 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 254 removed outlier: 4.074A pdb=" N LEU I 250 " --> pdb=" O ALA I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 260 through 276 removed outlier: 4.093A pdb=" N LEU I 264 " --> pdb=" O HIS I 260 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG I 270 " --> pdb=" O ARG I 266 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU I 271 " --> pdb=" O GLU I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 287 Processing helix chain 'I' and resid 298 through 310 removed outlier: 3.559A pdb=" N LEU I 303 " --> pdb=" O PHE I 299 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG I 308 " --> pdb=" O SER I 304 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU I 309 " --> pdb=" O LEU I 305 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU I 310 " --> pdb=" O LEU I 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 44 through 49 removed outlier: 4.327A pdb=" N ALA D 47 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ARG D 63 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE D 49 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA D 61 " --> pdb=" O PHE D 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 151 through 153 removed outlier: 5.588A pdb=" N LEU D 101 " --> pdb=" O PRO D 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 124 through 131 removed outlier: 6.211A pdb=" N VAL D 143 " --> pdb=" O ARG D 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 44 through 49 removed outlier: 5.195A pdb=" N VAL E 44 " --> pdb=" O ARG E 67 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG E 67 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA E 46 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG E 63 " --> pdb=" O GLU E 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.033A pdb=" N THR E 151 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.033A pdb=" N THR E 151 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL E 97 " --> pdb=" O ARG E 169 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ARG E 169 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE E 99 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL E 171 " --> pdb=" O CYS E 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 126 through 133 removed outlier: 3.777A pdb=" N GLU E 128 " --> pdb=" O VAL E 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 44 through 49 removed outlier: 6.372A pdb=" N ILE F 65 " --> pdb=" O VAL F 45 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA F 47 " --> pdb=" O ARG F 63 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ARG F 63 " --> pdb=" O ALA F 47 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE F 49 " --> pdb=" O ALA F 61 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA F 61 " --> pdb=" O PHE F 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 128 through 132 removed outlier: 3.796A pdb=" N SER F 141 " --> pdb=" O VAL F 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 170 through 173 Processing sheet with id=AB2, first strand: chain 'G' and resid 44 through 50 removed outlier: 6.568A pdb=" N ILE G 65 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA G 47 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG G 63 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE G 49 " --> pdb=" O ALA G 61 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA G 61 " --> pdb=" O PHE G 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 44 through 50 removed outlier: 6.568A pdb=" N ILE G 65 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA G 47 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG G 63 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE G 49 " --> pdb=" O ALA G 61 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA G 61 " --> pdb=" O PHE G 49 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU G 59 " --> pdb=" O CYS G 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 151 through 154 removed outlier: 3.712A pdb=" N THR G 151 " --> pdb=" O ALA G 102 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE G 99 " --> pdb=" O VAL G 167 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS G 165 " --> pdb=" O LEU G 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 125 through 131 removed outlier: 5.136A pdb=" N LYS G 126 " --> pdb=" O ARG G 147 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG G 147 " --> pdb=" O LYS G 126 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU G 128 " --> pdb=" O VAL G 145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 318 through 321 removed outlier: 3.537A pdb=" N ILE G 321 " --> pdb=" O LEU G 439 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU G 439 " --> pdb=" O ILE G 321 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 325 through 326 removed outlier: 3.892A pdb=" N THR G 425 " --> pdb=" O GLY G 369 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 44 through 49 removed outlier: 6.771A pdb=" N ILE H 65 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA H 47 " --> pdb=" O ARG H 63 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG H 63 " --> pdb=" O ALA H 47 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE H 49 " --> pdb=" O ALA H 61 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA H 61 " --> pdb=" O PHE H 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 151 through 154 removed outlier: 3.613A pdb=" N THR H 151 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU H 101 " --> pdb=" O PRO H 166 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 125 through 132 removed outlier: 3.508A pdb=" N VAL H 130 " --> pdb=" O VAL H 143 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL H 132 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER H 141 " --> pdb=" O VAL H 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 387 through 390 Processing sheet with id=AC3, first strand: chain 'I' and resid 44 through 49 removed outlier: 5.361A pdb=" N VAL I 44 " --> pdb=" O ARG I 67 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG I 67 " --> pdb=" O VAL I 44 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG I 63 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR I 72 " --> pdb=" O PHE I 68 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 58 through 59 Processing sheet with id=AC5, first strand: chain 'I' and resid 151 through 153 removed outlier: 3.581A pdb=" N THR I 151 " --> pdb=" O ALA I 102 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA I 102 " --> pdb=" O THR I 151 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL I 97 " --> pdb=" O ARG I 169 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG I 169 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE I 99 " --> pdb=" O VAL I 167 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL I 171 " --> pdb=" O CYS I 179 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 126 through 127 490 hydrogen bonds defined for protein. 1389 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: 4.89 Time building geometry restraints manager: 7.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5874 1.34 - 1.46: 3141 1.46 - 1.58: 8655 1.58 - 1.69: 0 1.69 - 1.81: 137 Bond restraints: 17807 Sorted by residual: bond pdb=" C SER H 370 " pdb=" N PRO H 371 " ideal model delta sigma weight residual 1.326 1.387 -0.060 1.44e-02 4.82e+03 1.76e+01 bond pdb=" C LEU G 14 " pdb=" N MET G 15 " ideal model delta sigma weight residual 1.333 1.278 0.055 1.59e-02 3.96e+03 1.19e+01 bond pdb=" C ASN D 81 " pdb=" N LEU D 82 " ideal model delta sigma weight residual 1.331 1.279 0.052 2.07e-02 2.33e+03 6.29e+00 bond pdb=" C HIS C 232 " pdb=" N PRO C 233 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.06e+00 bond pdb=" C ARG D 121 " pdb=" N PRO D 122 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.07e+00 ... (remaining 17802 not shown) Histogram of bond angle deviations from ideal: 98.98 - 106.68: 807 106.68 - 114.38: 10298 114.38 - 122.08: 9423 122.08 - 129.77: 3547 129.77 - 137.47: 198 Bond angle restraints: 24273 Sorted by residual: angle pdb=" C ARG G 67 " pdb=" N PHE G 68 " pdb=" CA PHE G 68 " ideal model delta sigma weight residual 120.68 131.95 -11.27 1.52e+00 4.33e-01 5.50e+01 angle pdb=" N ILE C 220 " pdb=" CA ILE C 220 " pdb=" C ILE C 220 " ideal model delta sigma weight residual 108.88 123.67 -14.79 2.16e+00 2.14e-01 4.69e+01 angle pdb=" N VAL C 324 " pdb=" CA VAL C 324 " pdb=" C VAL C 324 " ideal model delta sigma weight residual 112.17 105.71 6.46 9.50e-01 1.11e+00 4.63e+01 angle pdb=" C ARG C 219 " pdb=" N ILE C 220 " pdb=" CA ILE C 220 " ideal model delta sigma weight residual 122.13 134.38 -12.25 1.85e+00 2.92e-01 4.38e+01 angle pdb=" N MET G 256 " pdb=" CA MET G 256 " pdb=" C MET G 256 " ideal model delta sigma weight residual 109.81 120.98 -11.17 2.21e+00 2.05e-01 2.55e+01 ... (remaining 24268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.02: 10130 15.02 - 30.03: 612 30.03 - 45.05: 113 45.05 - 60.07: 18 60.07 - 75.08: 4 Dihedral angle restraints: 10877 sinusoidal: 4433 harmonic: 6444 Sorted by residual: dihedral pdb=" CA ILE C 220 " pdb=" C ILE C 220 " pdb=" N PRO C 221 " pdb=" CA PRO C 221 " ideal model delta harmonic sigma weight residual -180.00 -114.89 -65.11 0 5.00e+00 4.00e-02 1.70e+02 dihedral pdb=" CA TRP F 162 " pdb=" C TRP F 162 " pdb=" N LEU F 163 " pdb=" CA LEU F 163 " ideal model delta harmonic sigma weight residual 180.00 -124.15 -55.85 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA CYS C 310 " pdb=" C CYS C 310 " pdb=" N ARG C 311 " pdb=" CA ARG C 311 " ideal model delta harmonic sigma weight residual 180.00 127.03 52.97 0 5.00e+00 4.00e-02 1.12e+02 ... (remaining 10874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2430 0.096 - 0.192: 314 0.192 - 0.289: 12 0.289 - 0.385: 3 0.385 - 0.481: 1 Chirality restraints: 2760 Sorted by residual: chirality pdb=" CA HIS G 40 " pdb=" N HIS G 40 " pdb=" C HIS G 40 " pdb=" CB HIS G 40 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" CG LEU I 38 " pdb=" CB LEU I 38 " pdb=" CD1 LEU I 38 " pdb=" CD2 LEU I 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CB VAL G 234 " pdb=" CA VAL G 234 " pdb=" CG1 VAL G 234 " pdb=" CG2 VAL G 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 2757 not shown) Planarity restraints: 3184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 220 " -0.080 5.00e-02 4.00e+02 1.22e-01 2.37e+01 pdb=" N PRO C 221 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO C 221 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO C 221 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS G 40 " -0.057 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO G 41 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO G 41 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO G 41 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE I 299 " -0.050 5.00e-02 4.00e+02 7.46e-02 8.90e+00 pdb=" N PRO I 300 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO I 300 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO I 300 " -0.042 5.00e-02 4.00e+02 ... (remaining 3181 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3437 2.78 - 3.31: 15085 3.31 - 3.84: 26299 3.84 - 4.37: 29769 4.37 - 4.90: 50884 Nonbonded interactions: 125474 Sorted by model distance: nonbonded pdb=" OG SER F 119 " pdb=" O ARG F 121 " model vdw 2.248 2.440 nonbonded pdb=" ND1 HIS H 40 " pdb=" O PRO H 41 " model vdw 2.310 2.520 nonbonded pdb=" N ASP G 80 " pdb=" OD1 ASP G 80 " model vdw 2.331 2.520 nonbonded pdb=" NH1 ARG D 212 " pdb=" OE1 GLU D 247 " model vdw 2.336 2.520 nonbonded pdb=" O MET G 256 " pdb=" N TYR G 258 " model vdw 2.350 2.520 ... (remaining 125469 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 'D' and (resid 1 through 158 or (resid 159 through 161 and (name N or nam \ e CA or name C or name O or name CB )) or resid 162 through 311)) selection = (chain 'E' and (resid 1 through 158 or (resid 159 through 161 and (name N or nam \ e CA or name C or name O or name CB )) or resid 162 through 221 or (resid 222 th \ rough 225 and (name N or name CA or name C or name O or name CB )) or resid 226 \ through 311)) selection = (chain 'F' and (resid 1 through 221 or (resid 222 through 225 and (name N or nam \ e CA or name C or name O or name CB )) or resid 226 through 311)) selection = (chain 'I' and (resid 1 through 158 or (resid 159 through 161 and (name N or nam \ e CA or name C or name O or name CB )) or resid 162 through 221 or (resid 222 th \ rough 225 and (name N or name CA or name C or name O or name CB )) or resid 226 \ through 311)) } ncs_group { reference = (chain 'G' and (resid 1 through 333 or (resid 334 through 335 and (name N or nam \ e CA or name C or name O or name CB )) or resid 336 through 346 or (resid 347 an \ d (name N or name CA or name C or name O or name CB )) or resid 348 through 444) \ ) selection = chain 'H' } 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: 4.040 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: 19.620 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 45.230 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.080 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 0.077 17807 Z= 0.539 Angle : 1.187 17.170 24273 Z= 0.652 Chirality : 0.064 0.481 2760 Planarity : 0.010 0.122 3184 Dihedral : 10.340 75.082 6647 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.32 % Allowed : 13.45 % Favored : 86.23 % Rotamer: Outliers : 0.37 % Allowed : 2.17 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.36 % Twisted General : 0.88 % 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: -4.76 (0.14), residues: 2178 helix: -3.07 (0.13), residues: 681 sheet: -2.70 (0.25), residues: 330 loop : -3.43 (0.14), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP G 125 HIS 0.018 0.003 HIS H 206 PHE 0.029 0.003 PHE H 19 TYR 0.027 0.004 TYR G 427 ARG 0.013 0.001 ARG G 153 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 356 time to evaluate : 2.081 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 outliers start: 7 outliers final: 3 residues processed: 362 average time/residue: 0.3493 time to fit residues: 181.2177 Evaluate side-chains 188 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 185 time to evaluate : 1.829 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1462 time to fit residues: 3.3688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 10.0000 chunk 165 optimal weight: 0.4980 chunk 91 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 170 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 HIS D 148 HIS D 292 HIS ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN E 292 HIS F 40 HIS F 291 HIS F 292 HIS F 297 ASN G 157 GLN H 206 HIS ** H 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 HIS I 241 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17807 Z= 0.196 Angle : 0.734 14.051 24273 Z= 0.375 Chirality : 0.045 0.306 2760 Planarity : 0.007 0.116 3184 Dihedral : 7.516 59.078 2401 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.15 % Favored : 89.76 % Rotamer: Outliers : 0.05 % Allowed : 3.12 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.59 % 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: -3.58 (0.16), residues: 2178 helix: -1.46 (0.18), residues: 684 sheet: -2.17 (0.26), residues: 352 loop : -3.11 (0.15), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 162 HIS 0.009 0.001 HIS D 156 PHE 0.022 0.002 PHE H 426 TYR 0.016 0.002 TYR H 427 ARG 0.005 0.001 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 267 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 268 average time/residue: 0.3447 time to fit residues: 136.8712 Evaluate side-chains 188 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 2.400 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 110 optimal weight: 0.2980 chunk 61 optimal weight: 7.9990 chunk 164 optimal weight: 0.9980 chunk 134 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 198 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 196 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 159 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 292 HIS ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 GLN G 222 ASN I 17 GLN I 282 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17807 Z= 0.165 Angle : 0.668 13.962 24273 Z= 0.337 Chirality : 0.044 0.264 2760 Planarity : 0.006 0.075 3184 Dihedral : 6.766 52.058 2401 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.73 % Favored : 90.17 % Rotamer: Outliers : 0.05 % Allowed : 2.22 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.39 % 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: -2.87 (0.17), residues: 2178 helix: -0.54 (0.20), residues: 672 sheet: -1.91 (0.27), residues: 326 loop : -2.84 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G 125 HIS 0.007 0.001 HIS D 156 PHE 0.011 0.001 PHE E 13 TYR 0.010 0.001 TYR H 258 ARG 0.024 0.000 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 252 average time/residue: 0.3144 time to fit residues: 119.5804 Evaluate side-chains 184 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.962 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 195 optimal weight: 2.9990 chunk 149 optimal weight: 0.0980 chunk 102 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 199 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 HIS ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN G 157 GLN I 207 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17807 Z= 0.241 Angle : 0.683 11.501 24273 Z= 0.345 Chirality : 0.045 0.292 2760 Planarity : 0.006 0.081 3184 Dihedral : 6.694 53.354 2401 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.39 % Favored : 88.52 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.39 % 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: -2.58 (0.17), residues: 2178 helix: -0.12 (0.21), residues: 677 sheet: -1.81 (0.27), residues: 340 loop : -2.76 (0.16), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP G 42 HIS 0.010 0.001 HIS F 40 PHE 0.021 0.001 PHE G 237 TYR 0.017 0.001 TYR I 258 ARG 0.011 0.000 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 2.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.3085 time to fit residues: 112.0088 Evaluate side-chains 183 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 2.031 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 175 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 189 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 318 GLN ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN I 138 HIS I 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 17807 Z= 0.403 Angle : 0.820 11.080 24273 Z= 0.413 Chirality : 0.050 0.361 2760 Planarity : 0.007 0.069 3184 Dihedral : 7.192 57.424 2401 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.04 % Favored : 86.78 % Rotamer: Outliers : 0.05 % Allowed : 2.91 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.68 % Twisted General : 0.44 % 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: -2.64 (0.17), residues: 2178 helix: -0.15 (0.20), residues: 661 sheet: -1.89 (0.27), residues: 352 loop : -2.77 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP G 42 HIS 0.016 0.002 HIS F 40 PHE 0.023 0.002 PHE F 237 TYR 0.013 0.002 TYR H 427 ARG 0.013 0.001 ARG F 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 205 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 205 average time/residue: 0.3327 time to fit residues: 105.9432 Evaluate side-chains 168 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 1.924 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2206 time to fit residues: 2.9769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 70 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 0.0970 chunk 52 optimal weight: 6.9990 chunk 210 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 17 optimal weight: 0.0050 chunk 69 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 overall best weight: 1.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 292 HIS ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17807 Z= 0.219 Angle : 0.695 12.204 24273 Z= 0.350 Chirality : 0.046 0.279 2760 Planarity : 0.006 0.073 3184 Dihedral : 6.747 52.341 2401 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.15 % Favored : 89.81 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.34 % 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: -2.38 (0.18), residues: 2178 helix: 0.20 (0.21), residues: 661 sheet: -1.74 (0.28), residues: 344 loop : -2.70 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP I 238 HIS 0.009 0.001 HIS H 292 PHE 0.034 0.002 PHE H 426 TYR 0.014 0.001 TYR I 258 ARG 0.009 0.000 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.2977 time to fit residues: 101.8999 Evaluate side-chains 175 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.000 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 203 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 119 optimal weight: 0.6980 chunk 177 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 210 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 128 optimal weight: 0.2980 chunk 97 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 HIS ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17807 Z= 0.168 Angle : 0.663 11.811 24273 Z= 0.333 Chirality : 0.044 0.286 2760 Planarity : 0.005 0.066 3184 Dihedral : 6.372 51.566 2401 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.28 % Favored : 89.62 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.34 % 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: -2.15 (0.18), residues: 2178 helix: 0.49 (0.21), residues: 659 sheet: -1.61 (0.28), residues: 331 loop : -2.62 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP G 42 HIS 0.006 0.001 HIS E 292 PHE 0.025 0.001 PHE I 229 TYR 0.008 0.001 TYR G 265 ARG 0.008 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.3068 time to fit residues: 110.3180 Evaluate side-chains 191 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.038 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 143 optimal weight: 0.0970 chunk 103 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 165 optimal weight: 0.0770 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 292 HIS ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17807 Z= 0.166 Angle : 0.653 11.360 24273 Z= 0.326 Chirality : 0.043 0.269 2760 Planarity : 0.005 0.070 3184 Dihedral : 6.112 53.224 2401 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.69 % Favored : 90.13 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.25 % 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: -1.95 (0.18), residues: 2178 helix: 0.71 (0.21), residues: 665 sheet: -1.48 (0.29), residues: 314 loop : -2.54 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP I 238 HIS 0.006 0.001 HIS G 40 PHE 0.038 0.001 PHE H 426 TYR 0.012 0.001 TYR I 258 ARG 0.014 0.000 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.3363 time to fit residues: 121.0565 Evaluate side-chains 191 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.967 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 191 optimal weight: 0.8980 chunk 201 optimal weight: 10.0000 chunk 183 optimal weight: 0.5980 chunk 195 optimal weight: 9.9990 chunk 117 optimal weight: 0.0000 chunk 85 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 185 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 318 GLN D 292 HIS ** F 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17807 Z= 0.159 Angle : 0.644 11.484 24273 Z= 0.321 Chirality : 0.043 0.278 2760 Planarity : 0.005 0.101 3184 Dihedral : 5.971 53.506 2401 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.92 % Favored : 90.04 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.20 % 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: -1.78 (0.18), residues: 2178 helix: 0.97 (0.22), residues: 652 sheet: -1.49 (0.29), residues: 310 loop : -2.45 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP I 238 HIS 0.005 0.001 HIS H 292 PHE 0.024 0.001 PHE I 229 TYR 0.012 0.001 TYR G 265 ARG 0.007 0.000 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.3018 time to fit residues: 109.5740 Evaluate side-chains 197 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 2.256 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 207 optimal weight: 0.9990 chunk 126 optimal weight: 0.0970 chunk 98 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 217 optimal weight: 1.9990 chunk 199 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 292 HIS ** F 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17807 Z= 0.175 Angle : 0.657 11.252 24273 Z= 0.327 Chirality : 0.044 0.275 2760 Planarity : 0.005 0.101 3184 Dihedral : 5.921 53.317 2401 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.28 % Favored : 89.67 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.20 % 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: -1.77 (0.18), residues: 2178 helix: 0.91 (0.21), residues: 661 sheet: -1.46 (0.30), residues: 306 loop : -2.42 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP F 238 HIS 0.008 0.001 HIS F 40 PHE 0.025 0.001 PHE H 426 TYR 0.012 0.001 TYR G 265 ARG 0.007 0.000 ARG F 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 2.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2892 time to fit residues: 102.6968 Evaluate side-chains 195 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.980 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 173 optimal weight: 0.7980 chunk 72 optimal weight: 0.0870 chunk 177 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 292 HIS ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.100926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.081837 restraints weight = 49187.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.083818 restraints weight = 31228.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.085194 restraints weight = 22604.430| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17807 Z= 0.203 Angle : 0.669 12.366 24273 Z= 0.334 Chirality : 0.044 0.283 2760 Planarity : 0.005 0.096 3184 Dihedral : 5.975 53.462 2401 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.84 % Favored : 89.12 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.20 % 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: -1.74 (0.18), residues: 2178 helix: 0.89 (0.21), residues: 669 sheet: -1.43 (0.29), residues: 325 loop : -2.41 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.003 TRP F 238 HIS 0.014 0.001 HIS D 156 PHE 0.024 0.001 PHE I 229 TYR 0.012 0.001 TYR I 258 ARG 0.007 0.000 ARG F 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3486.15 seconds wall clock time: 64 minutes 25.41 seconds (3865.41 seconds total)