Starting phenix.real_space_refine on Thu Mar 14 17:34:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3f_22021/03_2024/6x3f_22021_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3f_22021/03_2024/6x3f_22021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3f_22021/03_2024/6x3f_22021.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3f_22021/03_2024/6x3f_22021.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3f_22021/03_2024/6x3f_22021_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3f_22021/03_2024/6x3f_22021_updated.pdb" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 66 5.16 5 C 6144 2.51 5 N 1488 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 39": "NH1" <-> "NH2" Residue "A GLU 40": "OE1" <-> "OE2" Residue "A ASP 275": "OD1" <-> "OD2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 353": "NH1" <-> "NH2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A ASP 388": "OD1" <-> "OD2" Residue "A GLU 469": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B GLU 40": "OE1" <-> "OE2" Residue "B ASP 275": "OD1" <-> "OD2" Residue "B PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B ARG 353": "NH1" <-> "NH2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 374": "OE1" <-> "OE2" Residue "B ASP 388": "OD1" <-> "OD2" Residue "B GLU 469": "OE1" <-> "OE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "C ARG 39": "NH1" <-> "NH2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C ASP 275": "OD1" <-> "OD2" Residue "C PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 280": "NH1" <-> "NH2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 342": "NH1" <-> "NH2" Residue "C ARG 353": "NH1" <-> "NH2" Residue "C PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 374": "OE1" <-> "OE2" Residue "C ASP 388": "OD1" <-> "OD2" Residue "C GLU 469": "OE1" <-> "OE2" Residue "C GLU 471": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9366 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3115 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 11, 'TRANS': 397} Chain breaks: 2 Chain: "B" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3115 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 11, 'TRANS': 397} Chain breaks: 2 Chain: "C" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3115 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 11, 'TRANS': 397} Chain breaks: 2 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.16, per 1000 atoms: 0.55 Number of scatterers: 9366 At special positions: 0 Unit cell: (115.648, 112.32, 77.376, 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 66 16.00 O 1668 8.00 N 1488 7.00 C 6144 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: 3.05 Conformation dependent library (CDL) restraints added in 1.8 seconds 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 3 sheets defined 64.8% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 19 through 39 removed outlier: 3.711A pdb=" N THR A 24 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 80 removed outlier: 3.679A pdb=" N LEU A 59 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 95 through 115 removed outlier: 4.034A pdb=" N THR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.982A pdb=" N ASP A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 212 through 228 removed outlier: 3.699A pdb=" N CYS A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 246 Processing helix chain 'A' and resid 251 through 272 removed outlier: 3.510A pdb=" N CYS A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.600A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 295 removed outlier: 3.937A pdb=" N GLY A 283 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 removed outlier: 3.774A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 319 removed outlier: 3.759A pdb=" N MET A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 330 removed outlier: 3.846A pdb=" N MET A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 removed outlier: 3.590A pdb=" N GLU A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 removed outlier: 4.370A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 384 removed outlier: 3.817A pdb=" N LEU A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 407 removed outlier: 3.524A pdb=" N THR A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 425 removed outlier: 3.583A pdb=" N THR A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.876A pdb=" N THR A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 457 removed outlier: 4.615A pdb=" N ARG A 445 " --> pdb=" O TRP A 441 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 39 removed outlier: 3.710A pdb=" N THR B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 80 removed outlier: 3.680A pdb=" N LEU B 59 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Proline residue: B 69 - end of helix Processing helix chain 'B' and resid 95 through 115 removed outlier: 4.034A pdb=" N THR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 104 " --> pdb=" O CYS B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 149 removed outlier: 3.982A pdb=" N ASP B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.699A pdb=" N CYS B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 246 Processing helix chain 'B' and resid 251 through 272 removed outlier: 3.510A pdb=" N CYS B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 3.600A pdb=" N PHE B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 295 removed outlier: 3.938A pdb=" N GLY B 283 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 removed outlier: 3.775A pdb=" N VAL B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 319 removed outlier: 3.759A pdb=" N MET B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 330 removed outlier: 3.846A pdb=" N MET B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 removed outlier: 3.589A pdb=" N GLU B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B 346 " --> pdb=" O ARG B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 358 removed outlier: 4.370A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 384 removed outlier: 3.817A pdb=" N LEU B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 407 removed outlier: 3.524A pdb=" N THR B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 425 removed outlier: 3.584A pdb=" N THR B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET B 419 " --> pdb=" O GLY B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.875A pdb=" N THR B 434 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 435 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 457 removed outlier: 4.614A pdb=" N ARG B 445 " --> pdb=" O TRP B 441 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 450 " --> pdb=" O PHE B 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 39 removed outlier: 3.711A pdb=" N THR C 24 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 80 removed outlier: 3.679A pdb=" N LEU C 59 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET C 60 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 66 " --> pdb=" O MET C 62 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Proline residue: C 69 - end of helix Processing helix chain 'C' and resid 95 through 115 removed outlier: 4.033A pdb=" N THR C 102 " --> pdb=" O TYR C 98 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 104 " --> pdb=" O CYS C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 149 removed outlier: 3.982A pdb=" N ASP C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 212 through 228 removed outlier: 3.698A pdb=" N CYS C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 246 Processing helix chain 'C' and resid 251 through 272 removed outlier: 3.510A pdb=" N CYS C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.600A pdb=" N PHE C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU C 272 " --> pdb=" O GLY C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 295 removed outlier: 3.937A pdb=" N GLY C 283 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 308 removed outlier: 3.774A pdb=" N VAL C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 319 removed outlier: 3.760A pdb=" N MET C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 330 removed outlier: 3.845A pdb=" N MET C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 347 removed outlier: 3.590A pdb=" N GLU C 345 " --> pdb=" O PHE C 341 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU C 346 " --> pdb=" O ARG C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 358 removed outlier: 4.370A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 384 removed outlier: 3.817A pdb=" N LEU C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL C 376 " --> pdb=" O LEU C 372 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 407 removed outlier: 3.525A pdb=" N THR C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER C 405 " --> pdb=" O ALA C 401 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 425 removed outlier: 3.582A pdb=" N THR C 418 " --> pdb=" O ALA C 414 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET C 419 " --> pdb=" O GLY C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 435 removed outlier: 3.876A pdb=" N THR C 434 " --> pdb=" O GLU C 431 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 435 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 457 removed outlier: 4.614A pdb=" N ARG C 445 " --> pdb=" O TRP C 441 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 450 " --> pdb=" O PHE C 446 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 164 through 167 Processing sheet with id= B, first strand: chain 'B' and resid 164 through 167 Processing sheet with id= C, first strand: chain 'C' and resid 164 through 167 435 hydrogen bonds defined for protein. 1287 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: 2.23 Time building geometry restraints manager: 3.40 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: 2847 1.34 - 1.46: 1329 1.46 - 1.57: 5208 1.57 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 9501 Sorted by residual: bond pdb=" C5 CHT A 601 " pdb=" N1 CHT A 601 " ideal model delta sigma weight residual 1.509 1.456 0.053 2.00e-02 2.50e+03 7.10e+00 bond pdb=" C5 CHT B 601 " pdb=" N1 CHT B 601 " ideal model delta sigma weight residual 1.509 1.456 0.053 2.00e-02 2.50e+03 7.02e+00 bond pdb=" C5 CHT C 601 " pdb=" N1 CHT C 601 " ideal model delta sigma weight residual 1.509 1.456 0.053 2.00e-02 2.50e+03 7.01e+00 bond pdb=" C7 CHT C 601 " pdb=" N1 CHT C 601 " ideal model delta sigma weight residual 1.492 1.451 0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" C8 CHT B 601 " pdb=" N1 CHT B 601 " ideal model delta sigma weight residual 1.492 1.451 0.041 2.00e-02 2.50e+03 4.11e+00 ... (remaining 9496 not shown) Histogram of bond angle deviations from ideal: 98.63 - 105.71: 183 105.71 - 112.80: 5149 112.80 - 119.89: 3531 119.89 - 126.97: 3965 126.97 - 134.06: 66 Bond angle restraints: 12894 Sorted by residual: angle pdb=" C VAL C 120 " pdb=" N THR C 121 " pdb=" CA THR C 121 " ideal model delta sigma weight residual 121.70 127.94 -6.24 1.80e+00 3.09e-01 1.20e+01 angle pdb=" C VAL B 120 " pdb=" N THR B 121 " pdb=" CA THR B 121 " ideal model delta sigma weight residual 121.70 127.91 -6.21 1.80e+00 3.09e-01 1.19e+01 angle pdb=" C VAL A 120 " pdb=" N THR A 121 " pdb=" CA THR A 121 " ideal model delta sigma weight residual 121.70 127.91 -6.21 1.80e+00 3.09e-01 1.19e+01 angle pdb=" C ASP B 388 " pdb=" N LEU B 389 " pdb=" CA LEU B 389 " ideal model delta sigma weight residual 121.54 127.45 -5.91 1.91e+00 2.74e-01 9.59e+00 angle pdb=" C ASP A 388 " pdb=" N LEU A 389 " pdb=" CA LEU A 389 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.53e+00 ... (remaining 12889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5124 17.91 - 35.83: 429 35.83 - 53.74: 96 53.74 - 71.65: 21 71.65 - 89.56: 6 Dihedral angle restraints: 5676 sinusoidal: 2160 harmonic: 3516 Sorted by residual: dihedral pdb=" CA VAL B 462 " pdb=" C VAL B 462 " pdb=" N GLU B 463 " pdb=" CA GLU B 463 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA THR A 247 " pdb=" C THR A 247 " pdb=" N MET A 248 " pdb=" CA MET A 248 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA THR B 247 " pdb=" C THR B 247 " pdb=" N MET B 248 " pdb=" CA MET B 248 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 5673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1380 0.071 - 0.143: 210 0.143 - 0.214: 42 0.214 - 0.286: 3 0.286 - 0.357: 3 Chirality restraints: 1638 Sorted by residual: chirality pdb=" CB VAL B 36 " pdb=" CA VAL B 36 " pdb=" CG1 VAL B 36 " pdb=" CG2 VAL B 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CB VAL C 36 " pdb=" CA VAL C 36 " pdb=" CG1 VAL C 36 " pdb=" CG2 VAL C 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CB VAL A 36 " pdb=" CA VAL A 36 " pdb=" CG1 VAL A 36 " pdb=" CG2 VAL A 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.15e+00 ... (remaining 1635 not shown) Planarity restraints: 1563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 258 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.83e+00 pdb=" N PRO B 259 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 259 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 259 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 258 " 0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO A 259 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 258 " 0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO C 259 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 259 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 259 " 0.037 5.00e-02 4.00e+02 ... (remaining 1560 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3228 2.86 - 3.37: 8889 3.37 - 3.88: 14895 3.88 - 4.39: 18266 4.39 - 4.90: 31078 Nonbonded interactions: 76356 Sorted by model distance: nonbonded pdb=" OH TYR B 98 " pdb=" OD1 ASP B 455 " model vdw 2.351 2.440 nonbonded pdb=" OH TYR A 98 " pdb=" OD1 ASP A 455 " model vdw 2.351 2.440 nonbonded pdb=" OH TYR C 98 " pdb=" OD1 ASP C 455 " model vdw 2.352 2.440 nonbonded pdb=" OH TYR C 373 " pdb=" OD1 ASP C 440 " model vdw 2.369 2.440 nonbonded pdb=" OH TYR A 373 " pdb=" OD1 ASP A 440 " model vdw 2.369 2.440 ... (remaining 76351 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.510 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.850 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.006 0.055 9501 Z= 0.384 Angle : 0.934 9.177 12894 Z= 0.489 Chirality : 0.058 0.357 1638 Planarity : 0.008 0.065 1563 Dihedral : 14.719 89.564 3408 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 13.51 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.78 (0.13), residues: 1209 helix: -4.59 (0.07), residues: 933 sheet: -3.31 (0.65), residues: 54 loop : -2.49 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 441 HIS 0.001 0.001 HIS C 41 PHE 0.011 0.002 PHE C 159 TYR 0.012 0.002 TYR C 162 ARG 0.005 0.001 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.046 Fit side-chains REVERT: A 149 MET cc_start: 0.8776 (mtt) cc_final: 0.8543 (mtp) REVERT: A 163 LYS cc_start: 0.8467 (tttm) cc_final: 0.8119 (tptp) REVERT: B 149 MET cc_start: 0.8755 (mtt) cc_final: 0.8534 (mtp) REVERT: B 163 LYS cc_start: 0.8481 (tttm) cc_final: 0.8244 (tmtt) REVERT: B 280 ARG cc_start: 0.6785 (ttt180) cc_final: 0.6295 (ttp-110) REVERT: B 306 PHE cc_start: 0.7504 (t80) cc_final: 0.7286 (t80) REVERT: B 307 ILE cc_start: 0.8214 (mm) cc_final: 0.8013 (mt) REVERT: C 149 MET cc_start: 0.8729 (mtt) cc_final: 0.8483 (mtp) REVERT: C 280 ARG cc_start: 0.6844 (ttt180) cc_final: 0.6472 (ttp-110) REVERT: C 307 ILE cc_start: 0.8236 (mm) cc_final: 0.7984 (mt) REVERT: C 342 ARG cc_start: 0.7488 (ttp80) cc_final: 0.7013 (ttp-170) REVERT: C 445 ARG cc_start: 0.7729 (mpt180) cc_final: 0.7518 (mpt180) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2440 time to fit residues: 56.7636 Evaluate side-chains 143 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.0970 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN B 347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9501 Z= 0.192 Angle : 0.565 6.579 12894 Z= 0.293 Chirality : 0.039 0.134 1638 Planarity : 0.005 0.040 1563 Dihedral : 5.264 27.049 1293 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.30 % Allowed : 14.38 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.18), residues: 1209 helix: -2.73 (0.13), residues: 930 sheet: -2.95 (0.65), residues: 54 loop : -2.64 (0.33), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 441 HIS 0.001 0.001 HIS B 41 PHE 0.023 0.001 PHE A 306 TYR 0.005 0.001 TYR A 373 ARG 0.005 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 144 time to evaluate : 1.053 Fit side-chains REVERT: A 149 MET cc_start: 0.8682 (mtt) cc_final: 0.8469 (mtp) REVERT: A 163 LYS cc_start: 0.8542 (tttm) cc_final: 0.8207 (tmtt) REVERT: A 262 ILE cc_start: 0.8027 (tt) cc_final: 0.7749 (tt) REVERT: B 41 HIS cc_start: 0.7171 (t70) cc_final: 0.6763 (m-70) REVERT: B 149 MET cc_start: 0.8683 (mtt) cc_final: 0.8468 (mtp) REVERT: B 306 PHE cc_start: 0.7616 (t80) cc_final: 0.7392 (t80) REVERT: B 342 ARG cc_start: 0.7640 (ttp80) cc_final: 0.7403 (ttp80) REVERT: C 21 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7286 (tp) REVERT: C 149 MET cc_start: 0.8729 (mtt) cc_final: 0.8484 (mtp) REVERT: C 298 ILE cc_start: 0.8723 (mm) cc_final: 0.8415 (mp) REVERT: C 325 LEU cc_start: 0.7520 (tt) cc_final: 0.6735 (mp) REVERT: C 342 ARG cc_start: 0.7542 (ttp80) cc_final: 0.7098 (ttp-170) outliers start: 34 outliers final: 20 residues processed: 169 average time/residue: 0.2076 time to fit residues: 48.9867 Evaluate side-chains 151 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 461 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 108 optimal weight: 0.0970 chunk 37 optimal weight: 0.2980 chunk 87 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN C 347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9501 Z= 0.161 Angle : 0.505 5.369 12894 Z= 0.258 Chirality : 0.039 0.131 1638 Planarity : 0.004 0.033 1563 Dihedral : 4.697 24.628 1293 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.33 % Allowed : 17.69 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.22), residues: 1209 helix: -1.54 (0.16), residues: 951 sheet: -2.52 (0.68), residues: 54 loop : -2.34 (0.37), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 441 HIS 0.001 0.001 HIS B 41 PHE 0.014 0.001 PHE A 306 TYR 0.009 0.001 TYR A 285 ARG 0.008 0.000 ARG B 353 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 1.011 Fit side-chains REVERT: A 163 LYS cc_start: 0.8578 (tttm) cc_final: 0.8220 (tmtt) REVERT: B 41 HIS cc_start: 0.7050 (t70) cc_final: 0.6798 (m-70) REVERT: B 149 MET cc_start: 0.8608 (mtt) cc_final: 0.8402 (mtp) REVERT: B 163 LYS cc_start: 0.8469 (tttm) cc_final: 0.8165 (tmtt) REVERT: B 329 MET cc_start: 0.6831 (mmp) cc_final: 0.6524 (mmm) REVERT: C 21 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7267 (tp) REVERT: C 149 MET cc_start: 0.8633 (mtt) cc_final: 0.8398 (mtp) REVERT: C 298 ILE cc_start: 0.8641 (mm) cc_final: 0.8434 (mp) REVERT: C 325 LEU cc_start: 0.7505 (tt) cc_final: 0.6854 (mp) REVERT: C 342 ARG cc_start: 0.7652 (ttp80) cc_final: 0.7205 (ttp-170) outliers start: 24 outliers final: 17 residues processed: 153 average time/residue: 0.2089 time to fit residues: 45.0904 Evaluate side-chains 150 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 462 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 12 optimal weight: 0.0010 chunk 52 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 ASN C 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9501 Z= 0.157 Angle : 0.492 7.796 12894 Z= 0.249 Chirality : 0.038 0.115 1638 Planarity : 0.003 0.027 1563 Dihedral : 4.412 21.136 1293 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.33 % Allowed : 18.37 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.24), residues: 1209 helix: -0.97 (0.17), residues: 942 sheet: -2.39 (0.68), residues: 54 loop : -1.98 (0.37), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 441 HIS 0.001 0.001 HIS B 41 PHE 0.021 0.001 PHE B 306 TYR 0.007 0.001 TYR A 285 ARG 0.006 0.000 ARG B 353 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 0.993 Fit side-chains REVERT: A 353 ARG cc_start: 0.5563 (mtm-85) cc_final: 0.5306 (mtm-85) REVERT: B 149 MET cc_start: 0.8520 (mtt) cc_final: 0.8318 (mtp) REVERT: B 163 LYS cc_start: 0.8464 (tttm) cc_final: 0.8160 (tmtt) REVERT: B 329 MET cc_start: 0.6775 (mmp) cc_final: 0.6556 (mmm) REVERT: B 442 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8750 (tt) REVERT: C 21 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7265 (tp) REVERT: C 149 MET cc_start: 0.8570 (mtt) cc_final: 0.8356 (mtp) REVERT: C 325 LEU cc_start: 0.7538 (tt) cc_final: 0.6937 (mp) REVERT: C 341 PHE cc_start: 0.6690 (OUTLIER) cc_final: 0.6455 (m-80) REVERT: C 342 ARG cc_start: 0.7668 (ttp80) cc_final: 0.7036 (ttp-170) outliers start: 24 outliers final: 16 residues processed: 153 average time/residue: 0.2005 time to fit residues: 43.6353 Evaluate side-chains 148 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 406 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 98 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 0.0970 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 HIS C 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9501 Z= 0.144 Angle : 0.474 6.875 12894 Z= 0.240 Chirality : 0.038 0.158 1638 Planarity : 0.003 0.025 1563 Dihedral : 4.220 18.403 1293 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.62 % Allowed : 19.14 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.24), residues: 1209 helix: -0.61 (0.17), residues: 942 sheet: -2.12 (0.72), residues: 54 loop : -1.75 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 19 HIS 0.001 0.000 HIS B 296 PHE 0.015 0.001 PHE C 306 TYR 0.006 0.001 TYR B 285 ARG 0.003 0.000 ARG B 353 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 1.088 Fit side-chains REVERT: A 262 ILE cc_start: 0.7847 (tt) cc_final: 0.7439 (tt) REVERT: A 353 ARG cc_start: 0.5582 (mtm-85) cc_final: 0.5299 (mtm-85) REVERT: B 149 MET cc_start: 0.8480 (mtt) cc_final: 0.8276 (mtp) REVERT: B 163 LYS cc_start: 0.8459 (tttm) cc_final: 0.8162 (tmtt) REVERT: B 329 MET cc_start: 0.6739 (mmp) cc_final: 0.6536 (mmm) REVERT: C 21 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7217 (tp) REVERT: C 149 MET cc_start: 0.8547 (mtt) cc_final: 0.8342 (mtp) REVERT: C 325 LEU cc_start: 0.7558 (tt) cc_final: 0.6928 (mp) outliers start: 27 outliers final: 18 residues processed: 155 average time/residue: 0.1945 time to fit residues: 42.8609 Evaluate side-chains 149 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 462 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9501 Z= 0.165 Angle : 0.488 8.606 12894 Z= 0.244 Chirality : 0.039 0.149 1638 Planarity : 0.003 0.025 1563 Dihedral : 4.167 14.717 1293 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.14 % Allowed : 19.73 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.25), residues: 1209 helix: -0.38 (0.18), residues: 939 sheet: -2.01 (0.73), residues: 54 loop : -1.59 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 19 HIS 0.001 0.001 HIS A 296 PHE 0.013 0.001 PHE C 306 TYR 0.007 0.001 TYR A 285 ARG 0.003 0.000 ARG C 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 1.112 Fit side-chains REVERT: A 262 ILE cc_start: 0.7856 (tt) cc_final: 0.7450 (tt) REVERT: A 353 ARG cc_start: 0.5710 (mtm-85) cc_final: 0.5403 (mtm-85) REVERT: B 149 MET cc_start: 0.8490 (mtt) cc_final: 0.8282 (mtp) REVERT: B 367 MET cc_start: 0.7160 (mtm) cc_final: 0.6931 (mtm) REVERT: C 21 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7221 (tp) REVERT: C 149 MET cc_start: 0.8561 (mtt) cc_final: 0.8358 (mtp) REVERT: C 325 LEU cc_start: 0.7524 (tt) cc_final: 0.6913 (mp) REVERT: C 341 PHE cc_start: 0.6709 (OUTLIER) cc_final: 0.6436 (m-80) outliers start: 22 outliers final: 15 residues processed: 148 average time/residue: 0.1939 time to fit residues: 41.4034 Evaluate side-chains 146 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 115 optimal weight: 0.4980 chunk 72 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9501 Z= 0.164 Angle : 0.483 8.299 12894 Z= 0.242 Chirality : 0.038 0.115 1638 Planarity : 0.003 0.036 1563 Dihedral : 4.106 15.480 1293 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.94 % Allowed : 20.41 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.25), residues: 1209 helix: -0.16 (0.18), residues: 939 sheet: -1.97 (0.74), residues: 54 loop : -1.56 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 19 HIS 0.001 0.000 HIS A 296 PHE 0.011 0.001 PHE C 306 TYR 0.007 0.001 TYR B 285 ARG 0.003 0.000 ARG C 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 0.983 Fit side-chains REVERT: A 262 ILE cc_start: 0.7845 (tt) cc_final: 0.7423 (tt) REVERT: A 353 ARG cc_start: 0.5748 (mtm-85) cc_final: 0.5446 (mtm-85) REVERT: B 149 MET cc_start: 0.8482 (mtt) cc_final: 0.8278 (mtp) REVERT: B 279 PHE cc_start: 0.7375 (m-80) cc_final: 0.7105 (m-80) REVERT: B 325 LEU cc_start: 0.7490 (tt) cc_final: 0.6846 (mp) REVERT: B 367 MET cc_start: 0.7152 (mtm) cc_final: 0.6894 (mtm) REVERT: B 437 ILE cc_start: 0.8285 (tp) cc_final: 0.7982 (tp) REVERT: C 21 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7169 (tp) REVERT: C 325 LEU cc_start: 0.7500 (tt) cc_final: 0.6889 (mp) outliers start: 20 outliers final: 17 residues processed: 152 average time/residue: 0.1821 time to fit residues: 40.8409 Evaluate side-chains 151 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 105 optimal weight: 0.0020 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9501 Z= 0.175 Angle : 0.489 8.873 12894 Z= 0.244 Chirality : 0.039 0.126 1638 Planarity : 0.003 0.038 1563 Dihedral : 4.114 17.825 1293 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.14 % Allowed : 20.02 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.25), residues: 1209 helix: -0.03 (0.18), residues: 939 sheet: -1.94 (0.74), residues: 54 loop : -1.53 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 19 HIS 0.001 0.000 HIS A 296 PHE 0.011 0.001 PHE A 240 TYR 0.007 0.001 TYR B 285 ARG 0.003 0.000 ARG C 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 1.043 Fit side-chains REVERT: A 262 ILE cc_start: 0.7830 (tt) cc_final: 0.7403 (tt) REVERT: A 353 ARG cc_start: 0.5720 (mtm-85) cc_final: 0.5426 (mtm-85) REVERT: B 149 MET cc_start: 0.8493 (mtt) cc_final: 0.8285 (mtp) REVERT: B 279 PHE cc_start: 0.7345 (m-80) cc_final: 0.7064 (m-80) REVERT: B 325 LEU cc_start: 0.7575 (tt) cc_final: 0.6908 (mp) REVERT: C 21 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7168 (tp) REVERT: C 325 LEU cc_start: 0.7538 (tt) cc_final: 0.6950 (mp) outliers start: 22 outliers final: 19 residues processed: 151 average time/residue: 0.1803 time to fit residues: 39.9130 Evaluate side-chains 153 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 70 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9501 Z= 0.289 Angle : 0.561 8.587 12894 Z= 0.275 Chirality : 0.041 0.190 1638 Planarity : 0.004 0.040 1563 Dihedral : 4.436 22.004 1293 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.14 % Allowed : 20.60 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.25), residues: 1209 helix: -0.14 (0.18), residues: 927 sheet: -1.86 (0.75), residues: 54 loop : -1.52 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 19 HIS 0.001 0.000 HIS A 41 PHE 0.016 0.002 PHE B 240 TYR 0.007 0.001 TYR A 206 ARG 0.003 0.000 ARG C 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 1.034 Fit side-chains REVERT: A 262 ILE cc_start: 0.7952 (tt) cc_final: 0.7523 (tt) REVERT: A 298 ILE cc_start: 0.8508 (mm) cc_final: 0.8230 (mt) REVERT: A 353 ARG cc_start: 0.5673 (mtm-85) cc_final: 0.5358 (mtm-85) REVERT: B 149 MET cc_start: 0.8598 (mtt) cc_final: 0.8371 (mtp) REVERT: B 279 PHE cc_start: 0.7362 (m-80) cc_final: 0.7067 (m-80) REVERT: B 307 ILE cc_start: 0.8203 (mm) cc_final: 0.8002 (mt) REVERT: B 367 MET cc_start: 0.7209 (mtm) cc_final: 0.6978 (mtm) REVERT: C 21 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7275 (tp) REVERT: C 307 ILE cc_start: 0.8150 (mm) cc_final: 0.7944 (mt) REVERT: C 325 LEU cc_start: 0.7549 (tt) cc_final: 0.6955 (mp) outliers start: 22 outliers final: 19 residues processed: 146 average time/residue: 0.1763 time to fit residues: 38.2495 Evaluate side-chains 145 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.4980 chunk 79 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9501 Z= 0.171 Angle : 0.502 8.599 12894 Z= 0.250 Chirality : 0.039 0.141 1638 Planarity : 0.003 0.039 1563 Dihedral : 4.216 21.572 1293 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.94 % Allowed : 20.89 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 1209 helix: 0.06 (0.18), residues: 942 sheet: -1.91 (0.74), residues: 54 loop : -1.70 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 19 HIS 0.001 0.000 HIS A 296 PHE 0.010 0.001 PHE A 240 TYR 0.006 0.001 TYR C 285 ARG 0.003 0.000 ARG C 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 0.984 Fit side-chains REVERT: A 262 ILE cc_start: 0.7899 (tt) cc_final: 0.7478 (tt) REVERT: A 353 ARG cc_start: 0.5631 (mtm-85) cc_final: 0.5355 (mtm-85) REVERT: B 149 MET cc_start: 0.8487 (mtt) cc_final: 0.8281 (mtp) REVERT: B 279 PHE cc_start: 0.7301 (m-80) cc_final: 0.6973 (m-80) REVERT: B 307 ILE cc_start: 0.8221 (mm) cc_final: 0.8005 (mt) REVERT: B 325 LEU cc_start: 0.7482 (tt) cc_final: 0.6829 (mp) REVERT: B 367 MET cc_start: 0.7185 (mtm) cc_final: 0.6982 (mtm) REVERT: C 21 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7186 (tp) REVERT: C 307 ILE cc_start: 0.8118 (mm) cc_final: 0.7915 (mt) REVERT: C 325 LEU cc_start: 0.7549 (tt) cc_final: 0.6946 (mp) outliers start: 20 outliers final: 18 residues processed: 146 average time/residue: 0.1799 time to fit residues: 38.4275 Evaluate side-chains 147 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 95 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 83 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.151362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.106173 restraints weight = 9991.199| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.98 r_work: 0.2968 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9501 Z= 0.120 Angle : 0.469 8.624 12894 Z= 0.236 Chirality : 0.038 0.116 1638 Planarity : 0.003 0.039 1563 Dihedral : 3.965 20.544 1293 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.87 % Allowed : 21.57 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1209 helix: 0.39 (0.18), residues: 936 sheet: -1.99 (0.73), residues: 54 loop : -1.57 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 441 HIS 0.001 0.000 HIS A 296 PHE 0.010 0.001 PHE B 306 TYR 0.006 0.001 TYR C 285 ARG 0.003 0.000 ARG C 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2076.42 seconds wall clock time: 37 minutes 50.27 seconds (2270.27 seconds total)