Starting phenix.real_space_refine on Sat Jul 20 00:21:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3f_22021/07_2024/6x3f_22021.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3f_22021/07_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_22021/07_2024/6x3f_22021.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3f_22021/07_2024/6x3f_22021.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3f_22021/07_2024/6x3f_22021.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3f_22021/07_2024/6x3f_22021.cif" } 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.41, per 1000 atoms: 0.58 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: 3.64 Conformation dependent library (CDL) restraints added in 1.6 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... Secondary structure from input PDB file: 63 helices and 6 sheets defined 72.9% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 18 through 40 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 81 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 96 through 116 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 138 through 150 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) removed outlier: 3.832A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 211 through 229 removed outlier: 3.699A pdb=" N CYS A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 247 removed outlier: 3.669A pdb=" N VAL A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 257 through 273 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 277 through 282 Processing helix chain 'A' and resid 282 through 296 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 300 through 309 removed outlier: 3.774A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.670A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.846A pdb=" N MET A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 348 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 351 through 359 removed outlier: 3.754A pdb=" N THR A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.657A pdb=" N ALA A 371 " --> pdb=" O MET A 367 " (cutoff:3.500A) 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 391 through 408 removed outlier: 3.728A pdb=" N ILE A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) 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 413 through 426 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 429 through 436 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 439 through 458 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 40 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 81 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 96 through 116 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 138 through 150 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) removed outlier: 3.832A pdb=" N PHE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 158 Processing helix chain 'B' and resid 211 through 229 removed outlier: 3.699A pdb=" N CYS B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.668A pdb=" N VAL B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 257 through 273 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 277 through 282 Processing helix chain 'B' and resid 282 through 296 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 300 through 309 removed outlier: 3.775A pdb=" N VAL B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 320 removed outlier: 3.669A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 removed outlier: 3.846A pdb=" N MET B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 348 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 351 through 359 removed outlier: 3.754A pdb=" N THR B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 385 removed outlier: 3.657A pdb=" N ALA B 371 " --> pdb=" O MET B 367 " (cutoff:3.500A) 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 391 through 408 removed outlier: 3.727A pdb=" N ILE B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) 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 413 through 426 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 429 through 436 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 439 through 458 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 40 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 81 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 96 through 116 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 138 through 150 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) removed outlier: 3.831A pdb=" N PHE C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 211 through 229 removed outlier: 3.698A pdb=" N CYS C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 247 removed outlier: 3.669A pdb=" N VAL C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 257 through 273 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 277 through 282 Processing helix chain 'C' and resid 282 through 296 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 300 through 309 removed outlier: 3.774A pdb=" N VAL C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.670A pdb=" N PHE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 331 removed outlier: 3.845A pdb=" N MET C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 348 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 351 through 359 removed outlier: 3.754A pdb=" N THR C 355 " --> pdb=" O ASP C 351 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 385 removed outlier: 3.657A pdb=" N ALA C 371 " --> pdb=" O MET C 367 " (cutoff:3.500A) 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 391 through 408 removed outlier: 3.727A pdb=" N ILE C 395 " --> pdb=" O ILE C 391 " (cutoff:3.500A) 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 413 through 426 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 429 through 436 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 439 through 458 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=AA1, first strand: chain 'A' and resid 160 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 167 Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AA4, first strand: chain 'B' and resid 164 through 167 Processing sheet with id=AA5, first strand: chain 'C' and resid 160 through 161 Processing sheet with id=AA6, first strand: chain 'C' and resid 164 through 167 517 hydrogen bonds defined for protein. 1497 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: 2.39 Time building geometry restraints manager: 3.98 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: 3219 2.86 - 3.37: 8826 3.37 - 3.88: 14813 3.88 - 4.39: 18117 4.39 - 4.90: 31053 Nonbonded interactions: 76028 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 76023 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: 1.300 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.020 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.790 ------------------------------------------------------------------------------- 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= 0.385 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 : 1.025 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: 0.2353 time to fit residues: 54.7785 Evaluate side-chains 143 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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: 4.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 413 GLN B 347 ASN B 385 ASN B 413 GLN C 347 ASN C 385 ASN C 413 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9501 Z= 0.214 Angle : 0.585 6.640 12894 Z= 0.305 Chirality : 0.040 0.139 1638 Planarity : 0.006 0.041 1563 Dihedral : 5.376 26.165 1293 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.92 % Allowed : 15.26 % Favored : 81.83 % 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: -4.48 (0.19), residues: 1209 helix: -2.70 (0.13), residues: 948 sheet: -3.07 (0.65), residues: 54 loop : -2.74 (0.35), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 441 HIS 0.001 0.000 HIS B 41 PHE 0.024 0.002 PHE A 306 TYR 0.006 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 185 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 155 time to evaluate : 0.978 Fit side-chains REVERT: A 149 MET cc_start: 0.8692 (mtt) cc_final: 0.8486 (mtp) REVERT: A 163 LYS cc_start: 0.8586 (tttm) cc_final: 0.8246 (tmtt) REVERT: A 262 ILE cc_start: 0.8049 (tt) cc_final: 0.7576 (pt) REVERT: A 367 MET cc_start: 0.7165 (mtm) cc_final: 0.6960 (mtm) REVERT: B 149 MET cc_start: 0.8684 (mtt) cc_final: 0.8470 (mtp) REVERT: B 280 ARG cc_start: 0.6887 (ttt180) cc_final: 0.6397 (ttp-110) REVERT: C 21 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7289 (tp) REVERT: C 149 MET cc_start: 0.8738 (mtt) cc_final: 0.8494 (mtp) REVERT: C 280 ARG cc_start: 0.6873 (ttt180) cc_final: 0.6492 (ttp-110) REVERT: C 298 ILE cc_start: 0.8687 (mm) cc_final: 0.8407 (mp) REVERT: C 325 LEU cc_start: 0.7484 (tt) cc_final: 0.6723 (mp) REVERT: C 342 ARG cc_start: 0.7634 (ttp80) cc_final: 0.7218 (ttp-170) outliers start: 30 outliers final: 18 residues processed: 175 average time/residue: 0.2426 time to fit residues: 57.7409 Evaluate side-chains 155 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 136 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 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 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 304 ILE 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: 1.9990 chunk 33 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 chunk 74 optimal weight: 0.9980 chunk 30 optimal weight: 0.0070 chunk 109 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9501 Z= 0.204 Angle : 0.547 7.781 12894 Z= 0.278 Chirality : 0.040 0.134 1638 Planarity : 0.004 0.036 1563 Dihedral : 4.937 23.202 1293 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.43 % Allowed : 18.56 % Favored : 79.01 % 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: -2.78 (0.22), residues: 1209 helix: -1.46 (0.16), residues: 945 sheet: -2.57 (0.69), residues: 54 loop : -2.40 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 441 HIS 0.002 0.001 HIS B 41 PHE 0.016 0.001 PHE B 306 TYR 0.007 0.001 TYR B 285 ARG 0.008 0.001 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 165 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 1.059 Fit side-chains REVERT: A 298 ILE cc_start: 0.8586 (mm) cc_final: 0.8339 (mt) REVERT: A 367 MET cc_start: 0.7158 (mtm) cc_final: 0.6906 (mtm) REVERT: B 41 HIS cc_start: 0.7034 (t70) cc_final: 0.6726 (m-70) REVERT: B 262 ILE cc_start: 0.7837 (tt) cc_final: 0.7627 (tt) REVERT: C 21 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7271 (tp) REVERT: C 149 MET cc_start: 0.8665 (mtt) cc_final: 0.8441 (mtp) REVERT: C 325 LEU cc_start: 0.7336 (tt) cc_final: 0.6569 (mp) REVERT: C 342 ARG cc_start: 0.7761 (ttp80) cc_final: 0.7378 (ttp-170) outliers start: 25 outliers final: 16 residues processed: 159 average time/residue: 0.2019 time to fit residues: 45.7210 Evaluate side-chains 152 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 71 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 328 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 115 optimal weight: 0.0050 chunk 57 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN B 312 ASN C 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2450 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= 0.145 Angle : 0.499 8.070 12894 Z= 0.255 Chirality : 0.039 0.116 1638 Planarity : 0.004 0.032 1563 Dihedral : 4.551 20.344 1293 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.75 % Allowed : 19.83 % Favored : 78.43 % 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: -1.93 (0.24), residues: 1209 helix: -0.86 (0.17), residues: 960 sheet: -2.51 (0.70), residues: 54 loop : -2.11 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 441 HIS 0.001 0.000 HIS B 41 PHE 0.018 0.001 PHE C 306 TYR 0.007 0.001 TYR A 285 ARG 0.009 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: 18 poor density : 141 time to evaluate : 0.934 Fit side-chains REVERT: A 367 MET cc_start: 0.7104 (mtm) cc_final: 0.6837 (mtm) REVERT: B 262 ILE cc_start: 0.7842 (tt) cc_final: 0.7576 (tt) REVERT: B 280 ARG cc_start: 0.6880 (ttt180) cc_final: 0.6415 (ttp-110) REVERT: C 21 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7268 (tp) REVERT: C 342 ARG cc_start: 0.7678 (ttp80) cc_final: 0.7142 (ttp-170) outliers start: 18 outliers final: 13 residues processed: 154 average time/residue: 0.2105 time to fit residues: 45.7262 Evaluate side-chains 152 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 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 328 LEU 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 406 ILE Chi-restraints excluded: chain C residue 462 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.2980 chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 0 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2616 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= 0.158 Angle : 0.499 7.075 12894 Z= 0.252 Chirality : 0.039 0.117 1638 Planarity : 0.003 0.027 1563 Dihedral : 4.405 16.442 1293 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.94 % Allowed : 20.70 % Favored : 77.36 % 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: -1.43 (0.25), residues: 1209 helix: -0.52 (0.17), residues: 960 sheet: -2.26 (0.73), residues: 54 loop : -1.86 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 441 HIS 0.000 0.000 HIS C 41 PHE 0.011 0.001 PHE C 306 TYR 0.004 0.001 TYR C 285 ARG 0.007 0.000 ARG C 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 154 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 1.144 Fit side-chains REVERT: A 262 ILE cc_start: 0.7853 (tt) cc_final: 0.7365 (tt) REVERT: B 262 ILE cc_start: 0.7892 (tt) cc_final: 0.7586 (tt) REVERT: B 353 ARG cc_start: 0.5607 (mtm-85) cc_final: 0.5406 (mtm-85) REVERT: B 446 PHE cc_start: 0.8086 (m-80) cc_final: 0.7773 (m-80) REVERT: C 21 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7209 (tp) REVERT: C 342 ARG cc_start: 0.7721 (ttp80) cc_final: 0.7192 (ttp-170) REVERT: C 353 ARG cc_start: 0.5474 (mtm-85) cc_final: 0.5264 (mtm180) outliers start: 20 outliers final: 16 residues processed: 151 average time/residue: 0.1918 time to fit residues: 42.3853 Evaluate side-chains 146 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 328 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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: 0.8064 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9501 Z= 0.261 Angle : 0.549 6.292 12894 Z= 0.275 Chirality : 0.041 0.124 1638 Planarity : 0.004 0.026 1563 Dihedral : 4.581 17.227 1293 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.43 % Allowed : 20.51 % Favored : 77.07 % 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: -1.23 (0.25), residues: 1209 helix: -0.42 (0.18), residues: 945 sheet: -2.13 (0.74), residues: 54 loop : -1.49 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 19 HIS 0.001 0.000 HIS C 41 PHE 0.015 0.002 PHE C 240 TYR 0.008 0.001 TYR C 285 ARG 0.005 0.000 ARG C 353 *********************** 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 159 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 1.095 Fit side-chains REVERT: A 262 ILE cc_start: 0.7967 (tt) cc_final: 0.7491 (tt) REVERT: B 262 ILE cc_start: 0.7926 (tt) cc_final: 0.7607 (tt) REVERT: B 353 ARG cc_start: 0.5632 (mtm-85) cc_final: 0.5366 (mtm-85) REVERT: C 21 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7280 (tp) REVERT: C 341 PHE cc_start: 0.6665 (OUTLIER) cc_final: 0.6337 (m-80) REVERT: C 342 ARG cc_start: 0.7622 (ttp80) cc_final: 0.7078 (ttp-170) REVERT: C 353 ARG cc_start: 0.5483 (mtm-85) cc_final: 0.5282 (mtm-85) outliers start: 25 outliers final: 20 residues processed: 153 average time/residue: 0.1878 time to fit residues: 41.9922 Evaluate side-chains 154 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 B residue 273 VAL Chi-restraints excluded: chain B residue 328 LEU 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 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: 0.0470 chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 84 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.6482 ------------------------------------------------------------------------------- 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: 0.2782 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= 0.148 Angle : 0.494 9.499 12894 Z= 0.249 Chirality : 0.038 0.119 1638 Planarity : 0.003 0.026 1563 Dihedral : 4.311 18.340 1293 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.33 % Allowed : 20.60 % Favored : 77.07 % 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: -0.89 (0.25), residues: 1209 helix: -0.16 (0.18), residues: 960 sheet: -2.17 (0.74), residues: 54 loop : -1.53 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 441 HIS 0.001 0.000 HIS B 41 PHE 0.009 0.001 PHE C 306 TYR 0.006 0.001 TYR C 285 ARG 0.005 0.000 ARG B 353 *********************** 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 158 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.051 Fit side-chains REVERT: A 262 ILE cc_start: 0.7913 (tt) cc_final: 0.7408 (tt) REVERT: A 328 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6605 (mp) REVERT: A 367 MET cc_start: 0.7010 (mtm) cc_final: 0.6793 (mtm) REVERT: B 262 ILE cc_start: 0.7717 (tt) cc_final: 0.7443 (tt) REVERT: B 353 ARG cc_start: 0.5638 (mtm-85) cc_final: 0.5412 (mtm-85) REVERT: B 446 PHE cc_start: 0.8105 (m-80) cc_final: 0.7798 (m-80) REVERT: C 21 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7164 (tp) REVERT: C 341 PHE cc_start: 0.6672 (OUTLIER) cc_final: 0.6414 (m-80) REVERT: C 342 ARG cc_start: 0.7690 (ttp80) cc_final: 0.7160 (ttp-170) REVERT: C 353 ARG cc_start: 0.5581 (mtm-85) cc_final: 0.5334 (mtm-85) outliers start: 24 outliers final: 18 residues processed: 152 average time/residue: 0.1836 time to fit residues: 40.9661 Evaluate side-chains 155 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 328 LEU 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 328 LEU 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 341 PHE 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: 0.8980 chunk 46 optimal weight: 0.6980 chunk 69 optimal weight: 0.0470 chunk 34 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 57 optimal weight: 0.1980 chunk 10 optimal weight: 0.1980 chunk 90 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- 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: 0.7968 moved from start: 0.2983 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= 0.121 Angle : 0.471 5.609 12894 Z= 0.240 Chirality : 0.038 0.116 1638 Planarity : 0.003 0.025 1563 Dihedral : 4.079 18.183 1293 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.75 % Allowed : 21.77 % Favored : 76.48 % 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: -0.53 (0.26), residues: 1209 helix: 0.11 (0.18), residues: 960 sheet: -2.25 (0.74), residues: 54 loop : -1.42 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 441 HIS 0.001 0.000 HIS C 41 PHE 0.015 0.001 PHE A 341 TYR 0.008 0.001 TYR C 257 ARG 0.004 0.000 ARG B 353 *********************** 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: 18 poor density : 137 time to evaluate : 1.049 Fit side-chains REVERT: A 262 ILE cc_start: 0.7852 (tt) cc_final: 0.7339 (tt) REVERT: A 328 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6673 (mp) REVERT: A 367 MET cc_start: 0.7018 (mtm) cc_final: 0.6798 (mtm) REVERT: B 262 ILE cc_start: 0.7744 (tt) cc_final: 0.7526 (tt) REVERT: C 60 MET cc_start: 0.8508 (mmp) cc_final: 0.8291 (mmt) REVERT: C 341 PHE cc_start: 0.6567 (OUTLIER) cc_final: 0.6309 (m-80) REVERT: C 353 ARG cc_start: 0.5611 (mtm-85) cc_final: 0.5362 (mtm-85) outliers start: 18 outliers final: 13 residues processed: 151 average time/residue: 0.1768 time to fit residues: 39.5358 Evaluate side-chains 145 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 328 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 341 PHE 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: 6.9990 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 113 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7992 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9501 Z= 0.156 Angle : 0.493 6.872 12894 Z= 0.248 Chirality : 0.039 0.117 1638 Planarity : 0.003 0.027 1563 Dihedral : 4.082 19.001 1293 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.65 % Allowed : 21.48 % Favored : 76.87 % 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: -0.41 (0.26), residues: 1209 helix: 0.20 (0.18), residues: 960 sheet: -2.19 (0.75), residues: 54 loop : -1.41 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 276 HIS 0.000 0.000 HIS C 296 PHE 0.030 0.001 PHE A 341 TYR 0.010 0.001 TYR C 285 ARG 0.007 0.000 ARG B 353 *********************** 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 147 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 0.959 Fit side-chains REVERT: A 262 ILE cc_start: 0.7895 (tt) cc_final: 0.7402 (tt) REVERT: A 328 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6686 (mp) REVERT: B 262 ILE cc_start: 0.7766 (tt) cc_final: 0.7531 (tt) REVERT: C 341 PHE cc_start: 0.6574 (OUTLIER) cc_final: 0.6232 (m-80) REVERT: C 353 ARG cc_start: 0.5552 (mtm-85) cc_final: 0.5315 (mtm-85) outliers start: 17 outliers final: 15 residues processed: 143 average time/residue: 0.1782 time to fit residues: 37.5932 Evaluate side-chains 146 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 328 LEU 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 207 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 341 PHE 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: 4.9990 chunk 79 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 95 optimal weight: 0.0770 chunk 9 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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: 0.7993 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9501 Z= 0.157 Angle : 0.488 5.375 12894 Z= 0.247 Chirality : 0.039 0.123 1638 Planarity : 0.003 0.031 1563 Dihedral : 4.089 19.746 1293 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.75 % Allowed : 21.38 % Favored : 76.87 % 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: -0.31 (0.26), residues: 1209 helix: 0.27 (0.18), residues: 963 sheet: -2.16 (0.75), residues: 54 loop : -1.46 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 441 HIS 0.000 0.000 HIS A 41 PHE 0.023 0.001 PHE A 341 TYR 0.016 0.001 TYR C 285 ARG 0.008 0.000 ARG B 353 ********************** 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: 18 poor density : 130 time to evaluate : 1.267 Fit side-chains REVERT: A 262 ILE cc_start: 0.7919 (tt) cc_final: 0.7418 (tt) REVERT: A 328 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6679 (mp) REVERT: B 262 ILE cc_start: 0.7775 (tt) cc_final: 0.7535 (tt) REVERT: C 341 PHE cc_start: 0.6560 (OUTLIER) cc_final: 0.6213 (m-80) REVERT: C 353 ARG cc_start: 0.5521 (mtm-85) cc_final: 0.5265 (mtm-85) REVERT: C 437 ILE cc_start: 0.7988 (tp) cc_final: 0.7582 (tp) outliers start: 18 outliers final: 16 residues processed: 144 average time/residue: 0.1835 time to fit residues: 39.1536 Evaluate side-chains 147 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 207 SER Chi-restraints excluded: chain A residue 328 LEU 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 207 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 341 PHE 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: 10.0000 chunk 14 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 0.0040 chunk 39 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 = 0.150687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.105635 restraints weight = 9955.117| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.96 r_work: 0.2940 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9501 Z= 0.141 Angle : 0.483 5.319 12894 Z= 0.244 Chirality : 0.038 0.115 1638 Planarity : 0.003 0.029 1563 Dihedral : 4.032 20.113 1293 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.75 % Allowed : 21.57 % Favored : 76.68 % 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: -0.09 (0.26), residues: 1209 helix: 0.44 (0.18), residues: 963 sheet: -2.17 (0.75), residues: 54 loop : -1.43 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 276 HIS 0.000 0.000 HIS A 41 PHE 0.022 0.001 PHE A 341 TYR 0.009 0.001 TYR C 285 ARG 0.007 0.000 ARG B 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2184.43 seconds wall clock time: 39 minutes 36.54 seconds (2376.54 seconds total)