Starting phenix.real_space_refine on Fri Sep 27 22:40:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj3_0010/09_2024/6gj3_0010.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj3_0010/09_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_0010/09_2024/6gj3_0010.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj3_0010/09_2024/6gj3_0010.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj3_0010/09_2024/6gj3_0010.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gj3_0010/09_2024/6gj3_0010.cif" } 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. Time to flip 12 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 11.18, per 1000 atoms: 0.64 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 - 3.00 Amino acid : True - 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: 3.45 Conformation dependent library (CDL) restraints added in 2.1 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: 1.74 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: 4.34 Time building geometry restraints manager: 4.14 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: 0.00 - 3.43: 23756 3.43 - 6.87: 462 6.87 - 10.30: 47 10.30 - 13.74: 5 13.74 - 17.17: 3 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 3.040 nonbonded pdb=" ND1 HIS H 40 " pdb=" O PRO H 41 " model vdw 2.310 3.120 nonbonded pdb=" N ASP G 80 " pdb=" OD1 ASP G 80 " model vdw 2.331 3.120 nonbonded pdb=" NH1 ARG D 212 " pdb=" OE1 GLU D 247 " model vdw 2.336 3.120 nonbonded pdb=" O MET G 256 " pdb=" N TYR G 258 " model vdw 2.350 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 37.520 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: 0.000 Extract box with map and model: 0.660 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 37.720 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.650 ------------------------------------------------------------------------------- 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 : 1.951 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: 0.3332 time to fit residues: 172.2611 Evaluate side-chains 197 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 193 time to evaluate : 1.915 ------------------------------------------------------------------------------- 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: 6.9990 chunk 165 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 197 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 HIS I 241 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17807 Z= 0.193 Angle : 0.742 14.155 24273 Z= 0.380 Chirality : 0.046 0.290 2760 Planarity : 0.007 0.117 3184 Dihedral : 7.468 59.063 2401 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.60 % Favored : 90.31 % Rotamer: Outliers : 0.05 % Allowed : 3.01 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.54 % 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: -3.56 (0.16), residues: 2178 helix: -1.46 (0.18), residues: 688 sheet: -2.12 (0.26), residues: 346 loop : -3.10 (0.15), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 162 HIS 0.010 0.001 HIS E 206 PHE 0.020 0.001 PHE H 426 TYR 0.016 0.002 TYR H 427 ARG 0.007 0.001 ARG I 259 *********************** 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 275 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 274 time to evaluate : 1.957 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: 0.5706 (mmt) cc_final: 0.5168 (mmt) REVERT: D 237 PHE cc_start: 0.7799 (p90) cc_final: 0.7482 (t80) REVERT: D 238 TRP cc_start: 0.7002 (m100) cc_final: 0.5979 (m100) REVERT: D 251 LYS cc_start: 0.8850 (tttt) cc_final: 0.8553 (ttpt) REVERT: E 292 HIS cc_start: 0.5161 (t-90) cc_final: 0.2993 (t-90) REVERT: F 184 PHE cc_start: 0.8462 (t80) cc_final: 0.8246 (t80) REVERT: F 238 TRP cc_start: 0.5160 (m100) cc_final: 0.4261 (m-90) REVERT: G 120 GLU cc_start: 0.7744 (pm20) cc_final: 0.7337 (pp20) REVERT: G 154 MET cc_start: 0.7617 (ttp) cc_final: 0.7332 (ttp) REVERT: G 367 LYS cc_start: 0.6469 (mttt) cc_final: 0.6229 (mtpp) REVERT: G 397 ILE cc_start: 0.5871 (mt) cc_final: 0.5526 (mt) REVERT: G 410 LEU cc_start: 0.5651 (mp) cc_final: 0.5238 (tt) REVERT: H 2 LYS cc_start: 0.8457 (mmtt) cc_final: 0.8120 (mmmm) REVERT: H 4 TYR cc_start: 0.8236 (m-10) cc_final: 0.8006 (m-80) REVERT: H 293 GLU cc_start: 0.8508 (pm20) cc_final: 0.8212 (mp0) REVERT: H 419 LEU cc_start: 0.8819 (mt) cc_final: 0.8347 (pp) REVERT: I 138 HIS cc_start: 0.8085 (p-80) cc_final: 0.7712 (p-80) REVERT: I 154 MET cc_start: 0.7294 (ppp) cc_final: 0.6686 (ppp) REVERT: I 258 TYR cc_start: 0.6958 (p90) cc_final: 0.6379 (p90) REVERT: I 263 LEU cc_start: 0.9139 (tt) cc_final: 0.8634 (mp) outliers start: 1 outliers final: 0 residues processed: 275 average time/residue: 0.3013 time to fit residues: 122.4056 Evaluate side-chains 194 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 2.089 ------------------------------------------------------------------------------- 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: 0.9990 chunk 61 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 198 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 196 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 HIS I 207 HIS I 282 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17807 Z= 0.313 Angle : 0.776 13.423 24273 Z= 0.391 Chirality : 0.048 0.326 2760 Planarity : 0.007 0.107 3184 Dihedral : 7.312 60.638 2401 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.71 % Favored : 88.20 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.68 % 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: -3.04 (0.17), residues: 2178 helix: -0.69 (0.19), residues: 681 sheet: -1.99 (0.26), residues: 353 loop : -2.96 (0.16), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP G 125 HIS 0.009 0.002 HIS G 40 PHE 0.019 0.002 PHE H 426 TYR 0.014 0.002 TYR G 427 ARG 0.023 0.001 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 228 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.972 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: 0.5409 (mmt) cc_final: 0.5133 (mmt) REVERT: D 238 TRP cc_start: 0.6968 (m100) cc_final: 0.6036 (m100) REVERT: D 251 LYS cc_start: 0.8905 (tttt) cc_final: 0.8586 (ttpt) REVERT: E 292 HIS cc_start: 0.5075 (t-90) cc_final: 0.4476 (t-90) REVERT: E 296 GLU cc_start: 0.8803 (mp0) cc_final: 0.8164 (tt0) REVERT: F 36 MET cc_start: 0.8991 (mmm) cc_final: 0.8612 (mtp) REVERT: G 120 GLU cc_start: 0.7555 (pm20) cc_final: 0.7195 (pp20) REVERT: G 154 MET cc_start: 0.7812 (ttp) cc_final: 0.7550 (ttp) REVERT: G 329 MET cc_start: 0.3913 (pmm) cc_final: 0.3656 (pmm) REVERT: G 367 LYS cc_start: 0.6365 (mttt) cc_final: 0.6129 (mtpt) REVERT: G 397 ILE cc_start: 0.5882 (mt) cc_final: 0.5510 (mt) REVERT: G 443 LEU cc_start: 0.8128 (mt) cc_final: 0.7926 (mm) REVERT: H 204 LEU cc_start: 0.8932 (tp) cc_final: 0.8589 (tt) REVERT: I 42 TRP cc_start: 0.6918 (m-10) cc_final: 0.6599 (m-10) REVERT: I 138 HIS cc_start: 0.8005 (p90) cc_final: 0.7661 (p-80) REVERT: I 258 TYR cc_start: 0.7258 (p90) cc_final: 0.6725 (p90) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.3140 time to fit residues: 106.5309 Evaluate side-chains 175 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.928 ------------------------------------------------------------------------------- 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: 0.7980 chunk 149 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 188 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2841 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= 0.202 Angle : 0.683 11.944 24273 Z= 0.347 Chirality : 0.045 0.314 2760 Planarity : 0.006 0.082 3184 Dihedral : 6.812 56.962 2401 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.73 % Favored : 90.22 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: -2.62 (0.17), residues: 2178 helix: -0.13 (0.20), residues: 679 sheet: -1.96 (0.27), residues: 338 loop : -2.76 (0.16), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP G 42 HIS 0.007 0.001 HIS H 292 PHE 0.017 0.001 PHE G 237 TYR 0.010 0.001 TYR H 405 ARG 0.009 0.000 ARG I 169 *********************** 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 249 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 2.103 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: 0.5770 (mmt) cc_final: 0.5490 (mmt) REVERT: D 238 TRP cc_start: 0.6981 (m100) cc_final: 0.5989 (m100) REVERT: D 251 LYS cc_start: 0.8969 (tttt) cc_final: 0.8652 (ttpt) REVERT: E 172 ARG cc_start: 0.5987 (ttp80) cc_final: 0.5758 (ttp80) REVERT: E 292 HIS cc_start: 0.5098 (t-90) cc_final: 0.4661 (t-90) REVERT: F 36 MET cc_start: 0.8869 (mmm) cc_final: 0.8586 (mtp) REVERT: F 184 PHE cc_start: 0.8548 (t80) cc_final: 0.8175 (t80) REVERT: G 26 ASP cc_start: 0.6848 (m-30) cc_final: 0.6081 (m-30) REVERT: G 120 GLU cc_start: 0.7682 (pm20) cc_final: 0.7378 (pp20) REVERT: G 154 MET cc_start: 0.7660 (ttp) cc_final: 0.7373 (ttp) REVERT: G 218 MET cc_start: 0.7077 (ttm) cc_final: 0.6789 (ttm) REVERT: G 324 LYS cc_start: 0.7162 (mmmm) cc_final: 0.6939 (mmtp) REVERT: G 397 ILE cc_start: 0.6209 (mt) cc_final: 0.5828 (mt) REVERT: G 434 ASP cc_start: 0.6672 (t70) cc_final: 0.6445 (t0) REVERT: G 436 LYS cc_start: 0.6858 (mptt) cc_final: 0.6035 (mtpt) REVERT: H 26 ASP cc_start: 0.7797 (t0) cc_final: 0.7070 (t0) REVERT: H 189 LEU cc_start: 0.9239 (mt) cc_final: 0.8938 (mp) REVERT: H 204 LEU cc_start: 0.8907 (tp) cc_final: 0.8633 (tt) REVERT: H 356 HIS cc_start: 0.5530 (t-90) cc_final: 0.5128 (t-90) REVERT: H 436 LYS cc_start: 0.7114 (mmpt) cc_final: 0.6881 (mmmt) REVERT: I 138 HIS cc_start: 0.7805 (p90) cc_final: 0.7451 (p-80) REVERT: I 258 TYR cc_start: 0.7267 (p90) cc_final: 0.6745 (p90) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.3143 time to fit residues: 115.3468 Evaluate side-chains 185 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.012 ------------------------------------------------------------------------------- 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: 1.9990 chunk 119 optimal weight: 0.9990 chunk 3 optimal weight: 0.0170 chunk 156 optimal weight: 4.9990 chunk 86 optimal weight: 0.0370 chunk 179 optimal weight: 4.9990 chunk 145 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS G 157 GLN ** I 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3223 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= 0.163 Angle : 0.660 15.726 24273 Z= 0.332 Chirality : 0.044 0.312 2760 Planarity : 0.005 0.066 3184 Dihedral : 6.380 55.496 2401 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: -2.32 (0.17), residues: 2178 helix: 0.19 (0.21), residues: 680 sheet: -1.69 (0.27), residues: 347 loop : -2.67 (0.16), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP G 42 HIS 0.004 0.001 HIS H 292 PHE 0.024 0.001 PHE H 362 TYR 0.008 0.001 TYR G 265 ARG 0.006 0.000 ARG H 219 *********************** 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 258 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 1.939 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: D 154 MET cc_start: 0.7254 (ttm) cc_final: 0.6948 (ttm) REVERT: D 238 TRP cc_start: 0.6873 (m100) cc_final: 0.5955 (m100) REVERT: D 251 LYS cc_start: 0.8985 (tttt) cc_final: 0.8701 (ttpt) REVERT: E 198 MET cc_start: 0.8222 (mmm) cc_final: 0.7535 (mtm) REVERT: E 292 HIS cc_start: 0.5113 (t-90) cc_final: 0.4179 (t-90) REVERT: F 184 PHE cc_start: 0.8539 (t80) cc_final: 0.8075 (t80) REVERT: F 196 SER cc_start: 0.8117 (m) cc_final: 0.7755 (t) REVERT: G 26 ASP cc_start: 0.6776 (m-30) cc_final: 0.6181 (m-30) REVERT: G 120 GLU cc_start: 0.7665 (pm20) cc_final: 0.7360 (pp20) REVERT: G 324 LYS cc_start: 0.7300 (mmmm) cc_final: 0.7087 (mmtp) REVERT: G 397 ILE cc_start: 0.6407 (mt) cc_final: 0.5845 (mt) REVERT: G 436 LYS cc_start: 0.6616 (mptt) cc_final: 0.5878 (mtpt) REVERT: H 26 ASP cc_start: 0.7929 (t0) cc_final: 0.7653 (t0) REVERT: H 204 LEU cc_start: 0.8866 (tp) cc_final: 0.8628 (tt) REVERT: H 329 MET cc_start: 0.7022 (mmp) cc_final: 0.6146 (mmt) REVERT: H 356 HIS cc_start: 0.5484 (t-90) cc_final: 0.5092 (t-90) REVERT: I 42 TRP cc_start: 0.6815 (m-10) cc_final: 0.6557 (m-10) REVERT: I 138 HIS cc_start: 0.7745 (p90) cc_final: 0.7485 (p-80) REVERT: I 154 MET cc_start: 0.6995 (ptm) cc_final: 0.6653 (ppp) REVERT: I 258 TYR cc_start: 0.7229 (p90) cc_final: 0.6678 (p90) REVERT: I 263 LEU cc_start: 0.9110 (tt) cc_final: 0.8841 (mp) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.3058 time to fit residues: 116.9098 Evaluate side-chains 198 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.086 ------------------------------------------------------------------------------- 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: 6.9990 chunk 189 optimal weight: 0.0870 chunk 41 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 210 optimal weight: 0.7980 chunk 175 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17807 Z= 0.273 Angle : 0.724 11.703 24273 Z= 0.361 Chirality : 0.046 0.298 2760 Planarity : 0.006 0.069 3184 Dihedral : 6.598 56.740 2401 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.39 % Favored : 88.57 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: -2.25 (0.18), residues: 2178 helix: 0.32 (0.21), residues: 663 sheet: -1.68 (0.27), residues: 359 loop : -2.63 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP I 238 HIS 0.010 0.001 HIS H 292 PHE 0.017 0.002 PHE E 13 TYR 0.011 0.002 TYR H 405 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 225 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 2.031 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: 0.7012 (m100) cc_final: 0.6043 (m100) REVERT: D 251 LYS cc_start: 0.9035 (tttt) cc_final: 0.8737 (ttpt) REVERT: E 292 HIS cc_start: 0.5120 (t-90) cc_final: 0.4380 (t-90) REVERT: E 296 GLU cc_start: 0.8836 (mp0) cc_final: 0.8098 (tt0) REVERT: F 184 PHE cc_start: 0.8559 (t80) cc_final: 0.8207 (t80) REVERT: G 15 MET cc_start: 0.7589 (mtt) cc_final: 0.7338 (mtt) REVERT: G 26 ASP cc_start: 0.6861 (m-30) cc_final: 0.6194 (m-30) REVERT: G 120 GLU cc_start: 0.7657 (pm20) cc_final: 0.7344 (pp20) REVERT: G 329 MET cc_start: 0.3721 (pmm) cc_final: 0.3465 (pmm) REVERT: G 397 ILE cc_start: 0.6003 (mt) cc_final: 0.5404 (mt) REVERT: G 436 LYS cc_start: 0.6950 (mptt) cc_final: 0.6193 (mtpt) REVERT: H 26 ASP cc_start: 0.7879 (t0) cc_final: 0.7085 (t0) REVERT: H 154 MET cc_start: 0.8089 (mpp) cc_final: 0.7781 (mpp) REVERT: H 356 HIS cc_start: 0.6035 (t-90) cc_final: 0.5304 (t-90) REVERT: H 419 LEU cc_start: 0.8694 (mm) cc_final: 0.8473 (mm) REVERT: H 436 LYS cc_start: 0.7108 (mmpt) cc_final: 0.6848 (mmmt) REVERT: I 42 TRP cc_start: 0.7032 (m-10) cc_final: 0.6729 (m-10) REVERT: I 258 TYR cc_start: 0.7293 (p90) cc_final: 0.6649 (p90) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.3133 time to fit residues: 105.2700 Evaluate side-chains 185 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.303 ------------------------------------------------------------------------------- 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: 2.9990 chunk 23 optimal weight: 0.4980 chunk 120 optimal weight: 4.9990 chunk 154 optimal weight: 0.3980 chunk 119 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 210 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 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 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN ** I 133 GLN ** 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: 0.7720 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17807 Z= 0.176 Angle : 0.661 17.194 24273 Z= 0.329 Chirality : 0.044 0.284 2760 Planarity : 0.005 0.065 3184 Dihedral : 6.281 55.190 2401 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.18 % Favored : 90.77 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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: -2.03 (0.18), residues: 2178 helix: 0.67 (0.21), residues: 653 sheet: -1.58 (0.28), residues: 336 loop : -2.56 (0.16), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP I 238 HIS 0.007 0.001 HIS H 292 PHE 0.028 0.001 PHE I 229 TYR 0.010 0.001 TYR H 405 ARG 0.005 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 233 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 2.175 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 129 ARG cc_start: 0.7881 (mtt90) cc_final: 0.7394 (mtm180) REVERT: D 238 TRP cc_start: 0.6879 (m100) cc_final: 0.6054 (m100) REVERT: D 251 LYS cc_start: 0.9022 (tttt) cc_final: 0.8712 (tttt) REVERT: E 198 MET cc_start: 0.8326 (mmm) cc_final: 0.7506 (mtm) REVERT: E 292 HIS cc_start: 0.5840 (t-90) cc_final: 0.4362 (t-90) REVERT: F 162 TRP cc_start: 0.7263 (t-100) cc_final: 0.6991 (t-100) REVERT: F 184 PHE cc_start: 0.8539 (t80) cc_final: 0.8100 (t80) REVERT: G 26 ASP cc_start: 0.6771 (m-30) cc_final: 0.6162 (m-30) REVERT: G 120 GLU cc_start: 0.7671 (pm20) cc_final: 0.7371 (pp20) REVERT: G 397 ILE cc_start: 0.6094 (mt) cc_final: 0.5399 (mt) REVERT: G 434 ASP cc_start: 0.5836 (t0) cc_final: 0.5600 (t0) REVERT: G 436 LYS cc_start: 0.6974 (mptt) cc_final: 0.6317 (mtpt) REVERT: H 26 ASP cc_start: 0.7962 (t0) cc_final: 0.7639 (t0) REVERT: H 154 MET cc_start: 0.8071 (mpp) cc_final: 0.7745 (mpp) REVERT: H 356 HIS cc_start: 0.6326 (t-90) cc_final: 0.5528 (t-90) REVERT: H 436 LYS cc_start: 0.7141 (mmpt) cc_final: 0.6904 (mmmt) REVERT: I 42 TRP cc_start: 0.6923 (m-10) cc_final: 0.6419 (m-10) REVERT: I 138 HIS cc_start: 0.8082 (p-80) cc_final: 0.7861 (p-80) REVERT: I 154 MET cc_start: 0.7083 (ptm) cc_final: 0.6716 (ppp) REVERT: I 258 TYR cc_start: 0.7155 (p90) cc_final: 0.6609 (p90) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.3099 time to fit residues: 107.8172 Evaluate side-chains 193 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.900 ------------------------------------------------------------------------------- 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: 0.9990 chunk 83 optimal weight: 0.0370 chunk 125 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 143 optimal weight: 0.0370 chunk 103 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS E 20 GLN ** 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: 0.7692 moved from start: 0.3721 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 : 0.640 11.795 24273 Z= 0.319 Chirality : 0.043 0.272 2760 Planarity : 0.005 0.065 3184 Dihedral : 6.028 53.499 2401 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.50 % Favored : 90.45 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % 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: -1.86 (0.18), residues: 2178 helix: 0.83 (0.22), residues: 658 sheet: -1.48 (0.28), residues: 324 loop : -2.48 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP I 238 HIS 0.006 0.001 HIS H 292 PHE 0.025 0.001 PHE I 229 TYR 0.010 0.001 TYR G 265 ARG 0.004 0.000 ARG I 259 *********************** 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 234 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.958 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 36 MET cc_start: 0.7694 (mtm) cc_final: 0.7461 (mtt) REVERT: D 129 ARG cc_start: 0.7891 (mtt90) cc_final: 0.7383 (mtm180) REVERT: D 238 TRP cc_start: 0.6895 (m100) cc_final: 0.6022 (m100) REVERT: D 251 LYS cc_start: 0.9024 (tttt) cc_final: 0.8753 (tttt) REVERT: E 198 MET cc_start: 0.8267 (mmm) cc_final: 0.7482 (mtm) REVERT: E 292 HIS cc_start: 0.5249 (t-90) cc_final: 0.4305 (t-90) REVERT: F 184 PHE cc_start: 0.8525 (t80) cc_final: 0.8057 (t80) REVERT: F 196 SER cc_start: 0.8108 (m) cc_final: 0.7730 (t) REVERT: G 26 ASP cc_start: 0.6734 (m-30) cc_final: 0.6120 (m-30) REVERT: G 120 GLU cc_start: 0.7637 (pm20) cc_final: 0.7381 (pp20) REVERT: G 324 LYS cc_start: 0.7174 (mmmm) cc_final: 0.6963 (mmtm) REVERT: G 329 MET cc_start: 0.3427 (pmm) cc_final: 0.3204 (pmm) REVERT: G 397 ILE cc_start: 0.6024 (mt) cc_final: 0.5287 (mt) REVERT: G 434 ASP cc_start: 0.5914 (t0) cc_final: 0.5632 (t0) REVERT: G 436 LYS cc_start: 0.6834 (mptt) cc_final: 0.6297 (mtpt) REVERT: H 26 ASP cc_start: 0.7957 (t0) cc_final: 0.7561 (t0) REVERT: H 329 MET cc_start: 0.6823 (mmp) cc_final: 0.5973 (mmt) REVERT: H 346 TRP cc_start: 0.7638 (m100) cc_final: 0.7335 (m100) REVERT: H 356 HIS cc_start: 0.6297 (t-90) cc_final: 0.5482 (t-90) REVERT: H 426 PHE cc_start: 0.5292 (t80) cc_final: 0.5034 (t80) REVERT: H 436 LYS cc_start: 0.7059 (mmpt) cc_final: 0.6853 (mmmt) REVERT: I 42 TRP cc_start: 0.6813 (m-10) cc_final: 0.6317 (m-10) REVERT: I 138 HIS cc_start: 0.8038 (p-80) cc_final: 0.7772 (p-80) REVERT: I 258 TYR cc_start: 0.7061 (p90) cc_final: 0.6573 (p90) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.3033 time to fit residues: 105.5699 Evaluate side-chains 191 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.907 ------------------------------------------------------------------------------- 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: 7.9990 chunk 183 optimal weight: 0.9990 chunk 195 optimal weight: 0.0770 chunk 117 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 185 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 231 HIS ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS E 20 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17807 Z= 0.190 Angle : 0.665 10.934 24273 Z= 0.330 Chirality : 0.044 0.284 2760 Planarity : 0.006 0.106 3184 Dihedral : 6.025 56.880 2401 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 0.96 (0.21), residues: 651 sheet: -1.44 (0.28), residues: 334 loop : -2.48 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP I 238 HIS 0.017 0.001 HIS D 156 PHE 0.025 0.001 PHE I 229 TYR 0.011 0.001 TYR G 265 ARG 0.005 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 223 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.978 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 129 ARG cc_start: 0.7806 (mtt90) cc_final: 0.7224 (mtm180) REVERT: D 237 PHE cc_start: 0.7784 (p90) cc_final: 0.7579 (t80) REVERT: D 238 TRP cc_start: 0.7027 (m100) cc_final: 0.6099 (m100) REVERT: D 251 LYS cc_start: 0.9012 (tttt) cc_final: 0.8713 (tttt) REVERT: E 75 ASP cc_start: 0.8482 (t0) cc_final: 0.8261 (t0) REVERT: E 292 HIS cc_start: 0.5664 (t-90) cc_final: 0.4300 (t-90) REVERT: F 184 PHE cc_start: 0.8539 (t80) cc_final: 0.8086 (t80) REVERT: G 26 ASP cc_start: 0.6744 (m-30) cc_final: 0.6169 (m-30) REVERT: G 120 GLU cc_start: 0.7633 (pm20) cc_final: 0.7382 (pp20) REVERT: G 397 ILE cc_start: 0.6146 (mt) cc_final: 0.5401 (mt) REVERT: G 434 ASP cc_start: 0.5866 (t0) cc_final: 0.5616 (t0) REVERT: G 436 LYS cc_start: 0.6747 (mptt) cc_final: 0.6175 (mtpt) REVERT: H 26 ASP cc_start: 0.7940 (t0) cc_final: 0.7224 (t0) REVERT: H 154 MET cc_start: 0.8050 (mpp) cc_final: 0.7779 (mpp) REVERT: H 329 MET cc_start: 0.6919 (mmp) cc_final: 0.6126 (mmt) REVERT: H 426 PHE cc_start: 0.5263 (t80) cc_final: 0.5021 (t80) REVERT: H 436 LYS cc_start: 0.7186 (mmpt) cc_final: 0.6911 (mmmt) REVERT: I 42 TRP cc_start: 0.6894 (m-90) cc_final: 0.6353 (m-10) REVERT: I 138 HIS cc_start: 0.8137 (p-80) cc_final: 0.7850 (p-80) REVERT: I 258 TYR cc_start: 0.7109 (p90) cc_final: 0.6558 (p90) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.3003 time to fit residues: 100.5677 Evaluate side-chains 187 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 2.051 ------------------------------------------------------------------------------- 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: 0.8980 chunk 126 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 217 optimal weight: 0.4980 chunk 199 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 17 optimal weight: 0.0870 chunk 133 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS E 20 GLN I 177 GLN ** 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: 0.7696 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17807 Z= 0.170 Angle : 0.657 11.749 24273 Z= 0.325 Chirality : 0.044 0.287 2760 Planarity : 0.005 0.100 3184 Dihedral : 5.908 58.342 2401 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -1.71 (0.18), residues: 2178 helix: 1.02 (0.21), residues: 657 sheet: -1.35 (0.28), residues: 334 loop : -2.45 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 162 HIS 0.015 0.001 HIS D 156 PHE 0.025 0.001 PHE I 229 TYR 0.010 0.001 TYR G 265 ARG 0.011 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 235 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 2.120 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 129 ARG cc_start: 0.7816 (mtt90) cc_final: 0.7261 (mtm180) REVERT: D 238 TRP cc_start: 0.6970 (m100) cc_final: 0.6068 (m100) REVERT: D 251 LYS cc_start: 0.9017 (tttt) cc_final: 0.8721 (tttt) REVERT: E 198 MET cc_start: 0.8451 (mmm) cc_final: 0.7395 (mtm) REVERT: E 292 HIS cc_start: 0.5146 (t-90) cc_final: 0.4289 (t-90) REVERT: F 184 PHE cc_start: 0.8541 (t80) cc_final: 0.8027 (t80) REVERT: G 26 ASP cc_start: 0.6713 (m-30) cc_final: 0.6141 (m-30) REVERT: G 120 GLU cc_start: 0.7681 (pm20) cc_final: 0.7435 (pp20) REVERT: G 190 THR cc_start: 0.8381 (p) cc_final: 0.7910 (t) REVERT: G 434 ASP cc_start: 0.5889 (t0) cc_final: 0.5663 (t0) REVERT: G 436 LYS cc_start: 0.6812 (mptt) cc_final: 0.6273 (mtpt) REVERT: H 26 ASP cc_start: 0.7972 (t0) cc_final: 0.7588 (t0) REVERT: H 154 MET cc_start: 0.8036 (mpp) cc_final: 0.7770 (mpp) REVERT: H 329 MET cc_start: 0.6896 (mmp) cc_final: 0.6114 (mmt) REVERT: H 346 TRP cc_start: 0.7634 (m100) cc_final: 0.7369 (m100) REVERT: H 353 MET cc_start: 0.4164 (ptp) cc_final: 0.3876 (ptp) REVERT: H 426 PHE cc_start: 0.5258 (t80) cc_final: 0.4953 (t80) REVERT: I 42 TRP cc_start: 0.6867 (m-90) cc_final: 0.6365 (m-10) REVERT: I 51 ASP cc_start: 0.6517 (p0) cc_final: 0.5844 (p0) REVERT: I 138 HIS cc_start: 0.8115 (p-80) cc_final: 0.7898 (p-80) REVERT: I 203 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7763 (tm-30) REVERT: I 258 TYR cc_start: 0.7068 (p90) cc_final: 0.6508 (p90) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.3196 time to fit residues: 111.8885 Evaluate side-chains 188 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 2.020 ------------------------------------------------------------------------------- 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: 3.9990 chunk 159 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 173 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 21 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 356 HIS ** 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 = 0.3524 r_free = 0.3524 target = 0.100406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.080879 restraints weight = 48866.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.082982 restraints weight = 30057.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.084377 restraints weight = 21315.038| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17807 Z= 0.225 Angle : 0.695 12.514 24273 Z= 0.344 Chirality : 0.045 0.287 2760 Planarity : 0.006 0.099 3184 Dihedral : 6.031 57.175 2401 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -1.68 (0.18), residues: 2178 helix: 1.03 (0.21), residues: 651 sheet: -1.30 (0.28), residues: 335 loop : -2.41 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP G 125 HIS 0.014 0.001 HIS D 156 PHE 0.024 0.001 PHE I 229 TYR 0.011 0.001 TYR G 265 ARG 0.006 0.000 ARG F 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3466.38 seconds wall clock time: 62 minutes 55.68 seconds (3775.68 seconds total)