Starting phenix.real_space_refine on Tue Apr 9 20:26:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj3_0010/04_2024/6gj3_0010.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj3_0010/04_2024/6gj3_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_0010/04_2024/6gj3_0010.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj3_0010/04_2024/6gj3_0010.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj3_0010/04_2024/6gj3_0010.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj3_0010/04_2024/6gj3_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 9.32, per 1000 atoms: 0.54 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: 7.05 Conformation dependent library (CDL) restraints added in 3.6 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: 1.48 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: 4.29 Time building geometry restraints manager: 7.39 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: 5.160 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: 19.950 Check model and map are aligned: 0.300 Set scattering table: 0.130 Process input model: 44.310 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 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: 73.810 ------------------------------------------------------------------------------- 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 : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 218 ARG cc_start: 0.7877 (ttt180) cc_final: 0.7649 (ttm170) REVERT: C 224 THR cc_start: 0.8284 (p) cc_final: 0.8073 (p) REVERT: C 319 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6350 (mm) REVERT: C 325 MET cc_start: 0.5595 (mmt) cc_final: 0.5303 (mmt) REVERT: D 237 PHE cc_start: 0.7946 (p90) cc_final: 0.7627 (t80) REVERT: D 238 TRP cc_start: 0.6927 (m100) cc_final: 0.6404 (m100) REVERT: D 251 LYS cc_start: 0.9063 (tttt) cc_final: 0.8659 (ttpt) REVERT: E 292 HIS cc_start: 0.4961 (t-90) cc_final: 0.4660 (t70) REVERT: F 198 MET cc_start: 0.8192 (mmm) cc_final: 0.7835 (mmt) REVERT: G 120 GLU cc_start: 0.7703 (pm20) cc_final: 0.7324 (pp20) REVERT: G 154 MET cc_start: 0.7808 (ttp) cc_final: 0.7468 (ttp) REVERT: G 367 LYS cc_start: 0.6536 (mttt) cc_final: 0.6135 (mtpt) REVERT: G 397 ILE cc_start: 0.5455 (mt) cc_final: 0.4936 (mt) REVERT: H 2 LYS cc_start: 0.8423 (mmtt) cc_final: 0.7801 (mmmm) REVERT: H 4 TYR cc_start: 0.8529 (m-10) cc_final: 0.7852 (m-10) REVERT: H 67 ARG cc_start: 0.8073 (mmm-85) cc_final: 0.7473 (mmm-85) REVERT: H 188 LEU cc_start: 0.9336 (mt) cc_final: 0.9088 (mt) REVERT: H 419 LEU cc_start: 0.8829 (mt) cc_final: 0.8325 (pp) REVERT: I 138 HIS cc_start: 0.8189 (p-80) cc_final: 0.7835 (p-80) REVERT: I 258 TYR cc_start: 0.7017 (p90) cc_final: 0.6369 (p90) REVERT: I 277 THR cc_start: 0.9123 (p) cc_final: 0.8864 (t) outliers start: 7 outliers final: 3 residues processed: 362 average time/residue: 0.3543 time to fit residues: 182.7405 Evaluate side-chains 197 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 193 time to evaluate : 2.525 ------------------------------------------------------------------------------- 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: 5.9990 chunk 165 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 197 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 148 HIS D 292 HIS ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN F 40 HIS F 291 HIS F 292 HIS F 297 ASN G 156 HIS 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17807 Z= 0.201 Angle : 0.737 14.068 24273 Z= 0.377 Chirality : 0.045 0.312 2760 Planarity : 0.007 0.117 3184 Dihedral : 7.564 59.409 2401 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.33 % Favored : 89.58 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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: -3.57 (0.16), residues: 2178 helix: -1.42 (0.18), residues: 685 sheet: -2.15 (0.26), residues: 348 loop : -3.13 (0.15), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 162 HIS 0.009 0.001 HIS F 40 PHE 0.020 0.001 PHE H 426 TYR 0.014 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 266 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 325 MET cc_start: 0.5703 (mmt) cc_final: 0.5166 (mmt) REVERT: D 238 TRP cc_start: 0.7019 (m100) cc_final: 0.5967 (m100) REVERT: D 251 LYS cc_start: 0.8865 (tttt) cc_final: 0.8562 (ttpt) REVERT: E 292 HIS cc_start: 0.5248 (t-90) cc_final: 0.2703 (t70) REVERT: E 293 GLU cc_start: 0.7673 (mp0) cc_final: 0.7289 (pm20) REVERT: G 120 GLU cc_start: 0.7641 (pm20) cc_final: 0.7264 (pp20) REVERT: G 154 MET cc_start: 0.7720 (ttp) cc_final: 0.7361 (ttp) REVERT: G 367 LYS cc_start: 0.6466 (mttt) cc_final: 0.6195 (mtpt) REVERT: G 397 ILE cc_start: 0.5898 (mt) cc_final: 0.5452 (mt) REVERT: H 2 LYS cc_start: 0.8472 (mmtt) cc_final: 0.8147 (mmmm) REVERT: H 4 TYR cc_start: 0.8218 (m-10) cc_final: 0.7981 (m-80) REVERT: I 138 HIS cc_start: 0.8068 (p-80) cc_final: 0.7802 (p-80) REVERT: I 154 MET cc_start: 0.7341 (ppp) cc_final: 0.6745 (ppp) REVERT: I 258 TYR cc_start: 0.7049 (p90) cc_final: 0.6578 (p90) REVERT: I 263 LEU cc_start: 0.9186 (tt) cc_final: 0.8637 (mp) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.3344 time to fit residues: 130.3861 Evaluate side-chains 191 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.912 ------------------------------------------------------------------------------- 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: 0.4980 chunk 61 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 54 optimal weight: 0.0570 chunk 198 optimal weight: 20.0000 chunk 214 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 196 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 159 optimal weight: 10.0000 overall best weight: 0.8500 ------------------------------------------------------------------------------- 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: 0.7700 moved from start: 0.2584 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= 0.172 Angle : 0.674 14.204 24273 Z= 0.340 Chirality : 0.044 0.275 2760 Planarity : 0.006 0.090 3184 Dihedral : 6.846 57.295 2401 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.19 % Favored : 89.76 % Rotamer: Outliers : 0.05 % Allowed : 2.43 % Favored : 97.52 % 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: -2.91 (0.17), residues: 2178 helix: -0.53 (0.20), residues: 672 sheet: -1.98 (0.27), residues: 333 loop : -2.87 (0.16), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 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 0.021 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 255 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 325 MET cc_start: 0.5655 (mmt) cc_final: 0.5321 (mmt) REVERT: D 238 TRP cc_start: 0.6994 (m100) cc_final: 0.6005 (m100) REVERT: D 251 LYS cc_start: 0.8918 (tttt) cc_final: 0.8576 (ttpt) REVERT: E 292 HIS cc_start: 0.5259 (t-90) cc_final: 0.2970 (t-90) REVERT: F 36 MET cc_start: 0.8904 (mmm) cc_final: 0.8532 (mtp) REVERT: F 42 TRP cc_start: 0.5426 (m100) cc_final: 0.4244 (m-10) REVERT: F 118 GLU cc_start: 0.7933 (pm20) cc_final: 0.7553 (mm-30) REVERT: F 184 PHE cc_start: 0.8495 (t80) cc_final: 0.8185 (t80) REVERT: G 120 GLU cc_start: 0.7656 (pm20) cc_final: 0.7321 (pp20) REVERT: G 154 MET cc_start: 0.7497 (ttp) cc_final: 0.7193 (ttp) REVERT: G 329 MET cc_start: 0.4026 (pmm) cc_final: 0.3703 (pmm) REVERT: G 397 ILE cc_start: 0.6128 (mt) cc_final: 0.5596 (mt) REVERT: G 436 LYS cc_start: 0.7160 (mmtt) cc_final: 0.6439 (mtpt) REVERT: G 443 LEU cc_start: 0.8047 (mt) cc_final: 0.7843 (mm) REVERT: H 204 LEU cc_start: 0.8914 (tp) cc_final: 0.8525 (tt) REVERT: I 42 TRP cc_start: 0.6807 (m-10) cc_final: 0.6469 (m-10) REVERT: I 138 HIS cc_start: 0.8154 (p-80) cc_final: 0.7798 (p-80) REVERT: I 258 TYR cc_start: 0.7247 (p90) cc_final: 0.6618 (p90) REVERT: I 263 LEU cc_start: 0.9151 (tt) cc_final: 0.8657 (mp) outliers start: 1 outliers final: 0 residues processed: 255 average time/residue: 0.3224 time to fit residues: 122.2261 Evaluate side-chains 188 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 2.190 ------------------------------------------------------------------------------- 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: 0.9980 chunk 149 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 94 optimal weight: 0.3980 chunk 133 optimal weight: 8.9990 chunk 199 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 188 optimal weight: 0.4980 chunk 56 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2997 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 : 0.648 11.782 24273 Z= 0.326 Chirality : 0.043 0.299 2760 Planarity : 0.006 0.065 3184 Dihedral : 6.442 54.732 2401 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.06 % Favored : 89.85 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: -2.51 (0.17), residues: 2178 helix: -0.07 (0.21), residues: 679 sheet: -1.70 (0.28), residues: 321 loop : -2.74 (0.16), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP G 42 HIS 0.007 0.001 HIS D 156 PHE 0.020 0.001 PHE G 237 TYR 0.007 0.001 TYR D 265 ARG 0.011 0.000 ARG I 121 *********************** 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 256 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 2.176 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: C 325 MET cc_start: 0.5723 (mmt) cc_final: 0.5386 (mmt) REVERT: D 238 TRP cc_start: 0.6932 (m100) cc_final: 0.6017 (m100) REVERT: D 251 LYS cc_start: 0.8956 (tttt) cc_final: 0.8636 (ttpt) REVERT: E 75 ASP cc_start: 0.8518 (t0) cc_final: 0.8265 (t0) REVERT: F 36 MET cc_start: 0.8846 (mmm) cc_final: 0.8554 (mtp) REVERT: F 184 PHE cc_start: 0.8463 (t80) cc_final: 0.8162 (t80) REVERT: F 196 SER cc_start: 0.8119 (m) cc_final: 0.7693 (t) REVERT: G 120 GLU cc_start: 0.7648 (pm20) cc_final: 0.7319 (pp20) REVERT: G 154 MET cc_start: 0.7443 (ttp) cc_final: 0.7161 (ttp) REVERT: G 397 ILE cc_start: 0.6210 (mt) cc_final: 0.5626 (mt) REVERT: G 434 ASP cc_start: 0.5799 (t0) cc_final: 0.5533 (t0) REVERT: G 436 LYS cc_start: 0.7208 (mmtt) cc_final: 0.6565 (mtpt) REVERT: H 204 LEU cc_start: 0.8895 (tp) cc_final: 0.8559 (tt) REVERT: H 329 MET cc_start: 0.6815 (mmp) cc_final: 0.6431 (mmt) REVERT: I 15 MET cc_start: 0.7567 (mtm) cc_final: 0.7362 (mtm) REVERT: I 42 TRP cc_start: 0.6838 (m-10) cc_final: 0.6517 (m-10) REVERT: I 138 HIS cc_start: 0.8204 (p-80) cc_final: 0.7885 (p-80) REVERT: I 154 MET cc_start: 0.6950 (ptm) cc_final: 0.6617 (ppp) REVERT: I 258 TYR cc_start: 0.7063 (p90) cc_final: 0.6489 (p90) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.3100 time to fit residues: 118.4635 Evaluate side-chains 193 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.276 ------------------------------------------------------------------------------- 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: 3.9990 chunk 119 optimal weight: 0.5980 chunk 3 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 189 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN G 157 GLN I 207 HIS ** I 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17807 Z= 0.252 Angle : 0.690 11.032 24273 Z= 0.346 Chirality : 0.045 0.280 2760 Planarity : 0.006 0.068 3184 Dihedral : 6.510 55.359 2401 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.25 % Favored : 88.61 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % 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: -2.33 (0.18), residues: 2178 helix: 0.15 (0.21), residues: 675 sheet: -1.61 (0.28), residues: 336 loop : -2.67 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP G 42 HIS 0.010 0.001 HIS F 40 PHE 0.011 0.002 PHE H 19 TYR 0.010 0.002 TYR F 258 ARG 0.008 0.001 ARG I 183 *********************** 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 226 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.997 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: D 154 MET cc_start: 0.7492 (ttm) cc_final: 0.7168 (ttm) REVERT: D 238 TRP cc_start: 0.6984 (m100) cc_final: 0.5993 (m100) REVERT: D 251 LYS cc_start: 0.9009 (tttt) cc_final: 0.8691 (ttpt) REVERT: E 198 MET cc_start: 0.8279 (mmm) cc_final: 0.7531 (mtm) REVERT: E 292 HIS cc_start: 0.4957 (t-90) cc_final: 0.4281 (t-90) REVERT: F 36 MET cc_start: 0.8900 (mmm) cc_final: 0.8618 (mtp) REVERT: G 120 GLU cc_start: 0.7596 (pm20) cc_final: 0.7291 (pp20) REVERT: G 154 MET cc_start: 0.7582 (ttp) cc_final: 0.7318 (ttp) REVERT: G 397 ILE cc_start: 0.6200 (mt) cc_final: 0.5684 (mt) REVERT: G 410 LEU cc_start: 0.7261 (tt) cc_final: 0.7021 (mp) REVERT: G 434 ASP cc_start: 0.5533 (t0) cc_final: 0.5295 (t0) REVERT: G 436 LYS cc_start: 0.7223 (mmtt) cc_final: 0.6592 (mtpt) REVERT: H 154 MET cc_start: 0.7988 (mpp) cc_final: 0.7746 (mpp) REVERT: H 204 LEU cc_start: 0.8914 (tp) cc_final: 0.8613 (tt) REVERT: H 329 MET cc_start: 0.6747 (mmp) cc_final: 0.6399 (mmt) REVERT: H 436 LYS cc_start: 0.7166 (mmpt) cc_final: 0.6947 (mmmt) REVERT: I 1 MET cc_start: 0.7833 (ttm) cc_final: 0.7554 (ttm) REVERT: I 42 TRP cc_start: 0.6992 (m-10) cc_final: 0.6704 (m-10) REVERT: I 138 HIS cc_start: 0.8203 (p-80) cc_final: 0.7936 (p-80) REVERT: I 258 TYR cc_start: 0.7035 (p90) cc_final: 0.6434 (p90) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.3126 time to fit residues: 105.5301 Evaluate side-chains 186 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 2.316 ------------------------------------------------------------------------------- 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: 3.9990 chunk 189 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 69 optimal weight: 0.0470 chunk 110 optimal weight: 0.9980 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 GLN ** 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: 0.7690 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17807 Z= 0.156 Angle : 0.638 12.038 24273 Z= 0.319 Chirality : 0.043 0.277 2760 Planarity : 0.005 0.061 3184 Dihedral : 6.170 54.323 2401 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.77 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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: -2.09 (0.18), residues: 2178 helix: 0.46 (0.21), residues: 668 sheet: -1.55 (0.29), residues: 304 loop : -2.55 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP G 42 HIS 0.005 0.001 HIS H 292 PHE 0.026 0.001 PHE I 229 TYR 0.011 0.001 TYR G 265 ARG 0.008 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 251 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 2.036 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: D 154 MET cc_start: 0.7353 (ttm) cc_final: 0.7038 (ttm) REVERT: D 238 TRP cc_start: 0.6974 (m100) cc_final: 0.6075 (m100) REVERT: D 251 LYS cc_start: 0.9003 (tttt) cc_final: 0.8682 (ttpt) REVERT: E 198 MET cc_start: 0.8225 (mmm) cc_final: 0.7460 (mtm) REVERT: E 292 HIS cc_start: 0.4993 (t-90) cc_final: 0.4283 (t-90) REVERT: F 36 MET cc_start: 0.8826 (mmm) cc_final: 0.8605 (mtp) REVERT: F 76 THR cc_start: 0.8621 (p) cc_final: 0.8413 (p) REVERT: F 184 PHE cc_start: 0.8454 (t80) cc_final: 0.8071 (t80) REVERT: F 196 SER cc_start: 0.7993 (m) cc_final: 0.7791 (t) REVERT: G 120 GLU cc_start: 0.7544 (pm20) cc_final: 0.7298 (pp20) REVERT: G 154 MET cc_start: 0.7720 (ttp) cc_final: 0.7515 (ttp) REVERT: G 320 PHE cc_start: 0.5187 (m-80) cc_final: 0.4953 (m-80) REVERT: G 324 LYS cc_start: 0.7092 (mmmm) cc_final: 0.6848 (mmtp) REVERT: G 329 MET cc_start: 0.3396 (pmm) cc_final: 0.3163 (pmm) REVERT: G 397 ILE cc_start: 0.6151 (mt) cc_final: 0.5499 (mt) REVERT: G 410 LEU cc_start: 0.7296 (tt) cc_final: 0.7021 (mp) REVERT: G 434 ASP cc_start: 0.5949 (t0) cc_final: 0.5746 (t0) REVERT: G 436 LYS cc_start: 0.7069 (mmtt) cc_final: 0.6472 (mtpt) REVERT: H 204 LEU cc_start: 0.8867 (tp) cc_final: 0.8589 (tt) REVERT: H 329 MET cc_start: 0.6652 (mmp) cc_final: 0.6289 (mmt) REVERT: H 418 MET cc_start: 0.7291 (tmm) cc_final: 0.7091 (tmm) REVERT: H 436 LYS cc_start: 0.7137 (mmpt) cc_final: 0.6931 (mmmt) REVERT: I 42 TRP cc_start: 0.6774 (m-10) cc_final: 0.6494 (m-10) REVERT: I 138 HIS cc_start: 0.8226 (p-80) cc_final: 0.7969 (p-80) REVERT: I 154 MET cc_start: 0.7014 (ptm) cc_final: 0.6661 (ppp) REVERT: I 258 TYR cc_start: 0.6986 (p90) cc_final: 0.6459 (p90) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.3245 time to fit residues: 122.3037 Evaluate side-chains 198 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.030 ------------------------------------------------------------------------------- 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: 4.9990 chunk 23 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 154 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 chunk 117 optimal weight: 0.2980 chunk 210 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 GLN ** 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: 0.7745 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17807 Z= 0.233 Angle : 0.672 11.244 24273 Z= 0.336 Chirality : 0.045 0.279 2760 Planarity : 0.006 0.069 3184 Dihedral : 6.230 53.920 2401 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.93 % Favored : 88.98 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.29 % 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: -2.06 (0.18), residues: 2178 helix: 0.50 (0.21), residues: 667 sheet: -1.54 (0.29), residues: 317 loop : -2.54 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP G 42 HIS 0.016 0.001 HIS F 40 PHE 0.025 0.002 PHE H 426 TYR 0.011 0.001 TYR H 427 ARG 0.005 0.000 ARG I 169 *********************** 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 233 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 2.260 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: D 154 MET cc_start: 0.7468 (ttm) cc_final: 0.7190 (ttm) REVERT: D 238 TRP cc_start: 0.7021 (m100) cc_final: 0.6044 (m100) REVERT: D 251 LYS cc_start: 0.9036 (tttt) cc_final: 0.8723 (ttpt) REVERT: E 75 ASP cc_start: 0.8575 (t0) cc_final: 0.8352 (t0) REVERT: E 292 HIS cc_start: 0.5064 (t-90) cc_final: 0.4397 (t-90) REVERT: F 36 MET cc_start: 0.8821 (mmm) cc_final: 0.8601 (mtp) REVERT: F 184 PHE cc_start: 0.8510 (t80) cc_final: 0.8185 (t80) REVERT: F 196 SER cc_start: 0.8049 (m) cc_final: 0.7785 (t) REVERT: G 15 MET cc_start: 0.7498 (mtt) cc_final: 0.7200 (mtt) REVERT: G 120 GLU cc_start: 0.7536 (pm20) cc_final: 0.7317 (pp20) REVERT: G 154 MET cc_start: 0.7941 (ttp) cc_final: 0.7679 (ttp) REVERT: G 324 LYS cc_start: 0.7067 (mmmm) cc_final: 0.6849 (mmtp) REVERT: G 397 ILE cc_start: 0.6116 (mt) cc_final: 0.5337 (mt) REVERT: G 410 LEU cc_start: 0.7354 (tt) cc_final: 0.7074 (mp) REVERT: G 436 LYS cc_start: 0.7166 (mmtt) cc_final: 0.6492 (mtpt) REVERT: H 204 LEU cc_start: 0.8888 (tp) cc_final: 0.8655 (tt) REVERT: H 329 MET cc_start: 0.6839 (mmp) cc_final: 0.6489 (mmt) REVERT: H 436 LYS cc_start: 0.7181 (mmpt) cc_final: 0.6940 (mmmt) REVERT: I 42 TRP cc_start: 0.6941 (m-10) cc_final: 0.6593 (m-10) REVERT: I 154 MET cc_start: 0.7244 (ptm) cc_final: 0.6698 (ppp) REVERT: I 258 TYR cc_start: 0.6995 (p90) cc_final: 0.6371 (p90) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.3106 time to fit residues: 108.1567 Evaluate side-chains 192 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 2.057 ------------------------------------------------------------------------------- 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: 0.9980 chunk 83 optimal weight: 0.5980 chunk 125 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.0060 chunk 133 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 GLN ** 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: 0.7704 moved from start: 0.3641 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= 0.165 Angle : 0.634 11.138 24273 Z= 0.317 Chirality : 0.043 0.305 2760 Planarity : 0.005 0.097 3184 Dihedral : 6.015 52.892 2401 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.23 % Favored : 90.73 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: -1.91 (0.18), residues: 2178 helix: 0.74 (0.21), residues: 659 sheet: -1.47 (0.29), residues: 311 loop : -2.50 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP G 42 HIS 0.013 0.001 HIS F 40 PHE 0.038 0.001 PHE H 426 TYR 0.011 0.001 TYR G 265 ARG 0.003 0.000 ARG I 169 *********************** 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 245 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.172 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: D 238 TRP cc_start: 0.7034 (m100) cc_final: 0.6058 (m100) REVERT: D 251 LYS cc_start: 0.9021 (tttt) cc_final: 0.8715 (ttpt) REVERT: E 198 MET cc_start: 0.8386 (mmm) cc_final: 0.7478 (mtm) REVERT: E 256 MET cc_start: 0.8743 (tpt) cc_final: 0.8535 (mmm) REVERT: F 184 PHE cc_start: 0.8481 (t80) cc_final: 0.8071 (t80) REVERT: G 99 ILE cc_start: 0.9045 (mm) cc_final: 0.8769 (mm) REVERT: G 154 MET cc_start: 0.7851 (ttp) cc_final: 0.7625 (ttp) REVERT: G 320 PHE cc_start: 0.5269 (m-80) cc_final: 0.4916 (m-80) REVERT: G 324 LYS cc_start: 0.7092 (mmmm) cc_final: 0.6865 (mmtp) REVERT: G 329 MET cc_start: 0.3454 (pmm) cc_final: 0.3176 (pmm) REVERT: G 410 LEU cc_start: 0.7331 (tt) cc_final: 0.7077 (mp) REVERT: G 434 ASP cc_start: 0.5804 (t0) cc_final: 0.5566 (t0) REVERT: G 436 LYS cc_start: 0.7071 (mmtt) cc_final: 0.6443 (mtpt) REVERT: H 204 LEU cc_start: 0.8863 (tp) cc_final: 0.8641 (tt) REVERT: H 329 MET cc_start: 0.6774 (mmp) cc_final: 0.6382 (mmt) REVERT: H 436 LYS cc_start: 0.7173 (mmpt) cc_final: 0.6922 (mmmt) REVERT: I 42 TRP cc_start: 0.6860 (m-10) cc_final: 0.6512 (m-10) REVERT: I 154 MET cc_start: 0.7103 (ptm) cc_final: 0.6624 (ppp) REVERT: I 258 TYR cc_start: 0.6959 (p90) cc_final: 0.6393 (p90) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.3165 time to fit residues: 117.6776 Evaluate side-chains 196 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.974 ------------------------------------------------------------------------------- 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: 0.9990 chunk 201 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 85 optimal weight: 0.4980 chunk 153 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 chunk 185 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- 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** F 244 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3788 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= 0.167 Angle : 0.636 10.991 24273 Z= 0.316 Chirality : 0.043 0.271 2760 Planarity : 0.005 0.094 3184 Dihedral : 5.886 51.563 2401 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.60 % Favored : 90.31 % Rotamer: Outliers : 0.05 % Allowed : 0.69 % Favored : 99.26 % 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: -1.80 (0.18), residues: 2178 helix: 0.83 (0.22), residues: 661 sheet: -1.38 (0.29), residues: 309 loop : -2.45 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP G 42 HIS 0.006 0.001 HIS F 40 PHE 0.019 0.001 PHE H 426 TYR 0.012 0.001 TYR G 265 ARG 0.004 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 240 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 239 time to evaluate : 2.058 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: D 238 TRP cc_start: 0.6988 (m100) cc_final: 0.6070 (m100) REVERT: D 251 LYS cc_start: 0.9016 (tttt) cc_final: 0.8744 (ttpt) REVERT: E 198 MET cc_start: 0.8373 (mmm) cc_final: 0.7474 (mtm) REVERT: E 292 HIS cc_start: 0.4889 (t-90) cc_final: 0.4513 (t-90) REVERT: F 184 PHE cc_start: 0.8486 (t80) cc_final: 0.8066 (t80) REVERT: F 256 MET cc_start: 0.6640 (mpp) cc_final: 0.6387 (mpp) REVERT: G 99 ILE cc_start: 0.9007 (mm) cc_final: 0.8722 (mm) REVERT: G 154 MET cc_start: 0.7837 (ttp) cc_final: 0.7617 (ttp) REVERT: G 320 PHE cc_start: 0.5238 (m-80) cc_final: 0.4897 (m-80) REVERT: G 434 ASP cc_start: 0.5751 (t0) cc_final: 0.5492 (t0) REVERT: G 436 LYS cc_start: 0.7033 (mmtt) cc_final: 0.6475 (mtpt) REVERT: H 204 LEU cc_start: 0.8869 (tp) cc_final: 0.8667 (tt) REVERT: H 329 MET cc_start: 0.6713 (mmp) cc_final: 0.6331 (mmt) REVERT: H 436 LYS cc_start: 0.7134 (mmpt) cc_final: 0.6923 (mmmt) REVERT: I 42 TRP cc_start: 0.6776 (m-10) cc_final: 0.6418 (m-10) REVERT: I 154 MET cc_start: 0.6997 (ptm) cc_final: 0.6554 (ppp) REVERT: I 258 TYR cc_start: 0.6915 (p90) cc_final: 0.6451 (p90) outliers start: 1 outliers final: 0 residues processed: 240 average time/residue: 0.3081 time to fit residues: 111.5926 Evaluate side-chains 201 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 2.016 ------------------------------------------------------------------------------- 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: 3.9990 chunk 98 optimal weight: 4.9990 chunk 143 optimal weight: 0.6980 chunk 217 optimal weight: 0.4980 chunk 199 optimal weight: 0.4980 chunk 172 optimal weight: 0.7980 chunk 17 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 chunk 106 optimal weight: 0.0370 chunk 137 optimal weight: 0.5980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS ** F 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17807 Z= 0.154 Angle : 0.639 11.596 24273 Z= 0.315 Chirality : 0.043 0.281 2760 Planarity : 0.005 0.084 3184 Dihedral : 5.725 50.744 2401 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 0.05 % Allowed : 0.05 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.15 % 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: -1.64 (0.18), residues: 2178 helix: 1.06 (0.22), residues: 655 sheet: -1.35 (0.30), residues: 296 loop : -2.36 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP G 42 HIS 0.005 0.001 HIS D 156 PHE 0.038 0.001 PHE H 426 TYR 0.012 0.001 TYR G 265 ARG 0.009 0.000 ARG I 259 ********************** 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 241 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 240 time to evaluate : 2.113 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: C 229 ARG cc_start: 0.7608 (ptm160) cc_final: 0.7365 (ptt180) REVERT: D 238 TRP cc_start: 0.7034 (m100) cc_final: 0.6159 (m100) REVERT: D 251 LYS cc_start: 0.9030 (tttt) cc_final: 0.8740 (tttt) REVERT: F 184 PHE cc_start: 0.8478 (t80) cc_final: 0.8004 (t80) REVERT: F 256 MET cc_start: 0.6647 (mpp) cc_final: 0.6381 (mpp) REVERT: G 99 ILE cc_start: 0.8899 (mm) cc_final: 0.8608 (mm) REVERT: G 410 LEU cc_start: 0.7216 (tt) cc_final: 0.6945 (mt) REVERT: G 434 ASP cc_start: 0.5755 (t0) cc_final: 0.5533 (t0) REVERT: G 436 LYS cc_start: 0.6950 (mmtt) cc_final: 0.6450 (mtpt) REVERT: H 329 MET cc_start: 0.6837 (mmp) cc_final: 0.6461 (mmt) REVERT: I 51 ASP cc_start: 0.6919 (p0) cc_final: 0.6606 (p0) REVERT: I 154 MET cc_start: 0.6862 (ptm) cc_final: 0.6516 (ppp) REVERT: I 258 TYR cc_start: 0.6828 (p90) cc_final: 0.6208 (p90) outliers start: 1 outliers final: 1 residues processed: 241 average time/residue: 0.3023 time to fit residues: 110.6861 Evaluate side-chains 200 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 1.888 ------------------------------------------------------------------------------- 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: 5.9990 chunk 52 optimal weight: 4.9990 chunk 159 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 72 optimal weight: 0.0870 chunk 177 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.102625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.083499 restraints weight = 48557.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.085555 restraints weight = 30573.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.086936 restraints weight = 21924.278| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4064 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= 0.163 Angle : 0.642 13.104 24273 Z= 0.316 Chirality : 0.043 0.268 2760 Planarity : 0.005 0.086 3184 Dihedral : 5.663 50.895 2401 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.27 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.15 % 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: -1.52 (0.18), residues: 2178 helix: 1.20 (0.22), residues: 655 sheet: -1.31 (0.30), residues: 301 loop : -2.31 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP G 42 HIS 0.005 0.001 HIS H 292 PHE 0.021 0.001 PHE G 237 TYR 0.012 0.001 TYR G 265 ARG 0.004 0.000 ARG F 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3576.69 seconds wall clock time: 66 minutes 15.62 seconds (3975.62 seconds total)