Starting phenix.real_space_refine on Thu Mar 14 17:52:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2l_22011/03_2024/6x2l_22011.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2l_22011/03_2024/6x2l_22011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2l_22011/03_2024/6x2l_22011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2l_22011/03_2024/6x2l_22011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2l_22011/03_2024/6x2l_22011.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2l_22011/03_2024/6x2l_22011.pdb" } resolution = 2.85 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 69 5.16 5 C 6159 2.51 5 N 1491 2.21 5 O 1677 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 PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A ASP 275": "OD1" <-> "OD2" Residue "A ARG 353": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ASP 444": "OD1" <-> "OD2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B GLU 40": "OE1" <-> "OE2" Residue "B PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B ASP 275": "OD1" <-> "OD2" Residue "B ARG 353": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ASP 444": "OD1" <-> "OD2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "C ARG 39": "NH1" <-> "NH2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 272": "OE1" <-> "OE2" Residue "C ASP 275": "OD1" <-> "OD2" Residue "C ARG 353": "NH1" <-> "NH2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C ASP 444": "OD1" <-> "OD2" Residue "C ARG 447": "NH1" <-> "NH2" Residue "C PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 9396 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3132 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 11, 'TRANS': 399} Chain breaks: 2 Chain: "B" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3132 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 11, 'TRANS': 399} Chain breaks: 2 Chain: "C" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3132 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 11, 'TRANS': 399} Chain breaks: 2 Time building chain proxies: 5.44, per 1000 atoms: 0.58 Number of scatterers: 9396 At special positions: 0 Unit cell: (113.984, 109.824, 82.368, 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 69 16.00 O 1677 8.00 N 1491 7.00 C 6159 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: 3.59 Conformation dependent library (CDL) restraints added in 1.9 seconds 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2280 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 6 sheets defined 81.3% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 21 through 40 removed outlier: 3.613A pdb=" N ALA A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.739A pdb=" N ALA A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 86 removed outlier: 3.580A pdb=" N LEU A 59 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 3.761A pdb=" N SER A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 117 removed outlier: 3.565A pdb=" N VAL A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.554A pdb=" N MET A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.531A 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 230 removed outlier: 3.517A pdb=" N GLY A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 273 Proline residue: A 259 - end of helix removed outlier: 3.631A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 299 removed outlier: 3.679A pdb=" N THR A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.623A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 319 removed outlier: 3.608A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 removed outlier: 3.548A pdb=" N THR A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 349 removed outlier: 4.158A pdb=" N ARG A 342 " --> pdb=" O PRO A 338 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 363 removed outlier: 4.179A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.595A pdb=" N VAL A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 401 removed outlier: 3.696A pdb=" N THR A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 406 removed outlier: 3.527A pdb=" N SER A 405 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 427 removed outlier: 3.592A pdb=" N MET A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 438 removed outlier: 3.995A pdb=" N ILE A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 3.594A pdb=" N LEU A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG A 445 " --> pdb=" O TRP A 441 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 40 removed outlier: 3.613A pdb=" N ALA B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 removed outlier: 3.739A pdb=" N ALA B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 86 removed outlier: 3.580A pdb=" N LEU B 59 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Proline residue: B 69 - end of helix removed outlier: 3.761A pdb=" N SER B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 117 removed outlier: 3.565A pdb=" N VAL B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.554A pdb=" N MET B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.531A 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 230 removed outlier: 3.518A pdb=" N GLY B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 273 Proline residue: B 259 - end of helix removed outlier: 3.631A pdb=" N PHE B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 299 removed outlier: 3.679A pdb=" N THR B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.624A pdb=" N VAL B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 319 removed outlier: 3.608A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 removed outlier: 3.549A pdb=" N THR B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 349 removed outlier: 4.158A pdb=" N ARG B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN B 347 " --> pdb=" O CYS B 343 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 363 removed outlier: 4.179A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Proline residue: B 360 - end of helix Processing helix chain 'B' and resid 367 through 385 removed outlier: 3.595A pdb=" N VAL B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.696A pdb=" N THR B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 406 removed outlier: 3.528A pdb=" N SER B 405 " --> pdb=" O THR B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 427 removed outlier: 3.592A pdb=" N MET B 419 " --> pdb=" O GLY B 415 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 438 removed outlier: 3.994A pdb=" N ILE B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 466 removed outlier: 3.595A pdb=" N LEU B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG B 445 " --> pdb=" O TRP B 441 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP B 455 " --> pdb=" O ASN B 451 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 40 removed outlier: 3.613A pdb=" N ALA C 27 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 53 removed outlier: 3.739A pdb=" N ALA C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 86 removed outlier: 3.579A pdb=" N LEU C 59 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS C 64 " --> pdb=" O MET C 60 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE C 66 " --> pdb=" O MET C 62 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Proline residue: C 69 - end of helix removed outlier: 3.762A pdb=" N SER C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 117 removed outlier: 3.565A pdb=" N VAL C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.555A pdb=" N MET C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.531A 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 230 removed outlier: 3.518A pdb=" N GLY C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 273 Proline residue: C 259 - end of helix removed outlier: 3.631A pdb=" N PHE C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU C 272 " --> pdb=" O GLY C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 299 removed outlier: 3.678A pdb=" N THR C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 309 removed outlier: 3.622A pdb=" N VAL C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 319 removed outlier: 3.608A pdb=" N PHE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 330 removed outlier: 3.548A pdb=" N THR C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 349 removed outlier: 4.158A pdb=" N ARG C 342 " --> pdb=" O PRO C 338 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN C 347 " --> pdb=" O CYS C 343 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 363 removed outlier: 4.179A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Proline residue: C 360 - end of helix Processing helix chain 'C' and resid 367 through 385 removed outlier: 3.595A pdb=" N VAL C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 401 removed outlier: 3.696A pdb=" N THR C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 406 removed outlier: 3.527A pdb=" N SER C 405 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 427 removed outlier: 3.592A pdb=" N MET C 419 " --> pdb=" O GLY C 415 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 432 removed outlier: 3.589A pdb=" N ASP C 432 " --> pdb=" O PRO C 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 429 through 432' Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 439 through 466 removed outlier: 3.594A pdb=" N LEU C 443 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG C 445 " --> pdb=" O TRP C 441 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N PHE C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET C 449 " --> pdb=" O ARG C 445 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP C 455 " --> pdb=" O ASN C 451 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS C 464 " --> pdb=" O GLY C 460 " (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 167 624 hydrogen bonds defined for protein. 1836 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: 2.69 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1670 1.32 - 1.45: 2168 1.45 - 1.57: 5573 1.57 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 9534 Sorted by residual: bond pdb=" C MET C 419 " pdb=" O MET C 419 " ideal model delta sigma weight residual 1.237 1.200 0.037 1.19e-02 7.06e+03 9.55e+00 bond pdb=" C MET A 419 " pdb=" O MET A 419 " ideal model delta sigma weight residual 1.237 1.200 0.036 1.19e-02 7.06e+03 9.28e+00 bond pdb=" C MET B 419 " pdb=" O MET B 419 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.19e-02 7.06e+03 9.09e+00 bond pdb=" N LEU B 372 " pdb=" CA LEU B 372 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.41e+00 bond pdb=" N LEU A 372 " pdb=" CA LEU A 372 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.20e+00 ... (remaining 9529 not shown) Histogram of bond angle deviations from ideal: 97.94 - 105.14: 171 105.14 - 112.34: 4890 112.34 - 119.54: 3415 119.54 - 126.73: 4391 126.73 - 133.93: 69 Bond angle restraints: 12936 Sorted by residual: angle pdb=" C ASP C 388 " pdb=" N LEU C 389 " pdb=" CA LEU C 389 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C ASP A 388 " pdb=" N LEU A 389 " pdb=" CA LEU A 389 " ideal model delta sigma weight residual 121.54 128.87 -7.33 1.91e+00 2.74e-01 1.47e+01 angle pdb=" C ASP B 388 " pdb=" N LEU B 389 " pdb=" CA LEU B 389 " ideal model delta sigma weight residual 121.54 128.84 -7.30 1.91e+00 2.74e-01 1.46e+01 angle pdb=" CB MET C 473 " pdb=" CG MET C 473 " pdb=" SD MET C 473 " ideal model delta sigma weight residual 112.70 103.26 9.44 3.00e+00 1.11e-01 9.89e+00 angle pdb=" CB MET A 473 " pdb=" CG MET A 473 " pdb=" SD MET A 473 " ideal model delta sigma weight residual 112.70 103.30 9.40 3.00e+00 1.11e-01 9.82e+00 ... (remaining 12931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 5150 16.78 - 33.56: 430 33.56 - 50.35: 96 50.35 - 67.13: 21 67.13 - 83.91: 9 Dihedral angle restraints: 5706 sinusoidal: 2172 harmonic: 3534 Sorted by residual: dihedral pdb=" CA LEU A 384 " pdb=" C LEU A 384 " pdb=" N ASN A 385 " pdb=" CA ASN A 385 " ideal model delta harmonic sigma weight residual 180.00 160.52 19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LEU C 384 " pdb=" C LEU C 384 " pdb=" N ASN C 385 " pdb=" CA ASN C 385 " ideal model delta harmonic sigma weight residual 180.00 160.53 19.47 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LEU B 384 " pdb=" C LEU B 384 " pdb=" N ASN B 385 " pdb=" CA ASN B 385 " ideal model delta harmonic sigma weight residual 180.00 160.54 19.46 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 847 0.039 - 0.077: 565 0.077 - 0.116: 154 0.116 - 0.154: 59 0.154 - 0.193: 19 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CB VAL C 433 " pdb=" CA VAL C 433 " pdb=" CG1 VAL C 433 " pdb=" CG2 VAL C 433 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.28e-01 chirality pdb=" CB VAL B 433 " pdb=" CA VAL B 433 " pdb=" CG1 VAL B 433 " pdb=" CG2 VAL B 433 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" CB VAL A 433 " pdb=" CA VAL A 433 " pdb=" CG1 VAL A 433 " pdb=" CG2 VAL A 433 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.92e-01 ... (remaining 1641 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 301 " -0.049 5.00e-02 4.00e+02 7.26e-02 8.43e+00 pdb=" N PRO C 302 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 302 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 302 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 301 " -0.049 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO B 302 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 302 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 302 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 301 " -0.049 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO A 302 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " -0.041 5.00e-02 4.00e+02 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 60 2.64 - 3.21: 8450 3.21 - 3.77: 14468 3.77 - 4.34: 20729 4.34 - 4.90: 33676 Nonbonded interactions: 77383 Sorted by model distance: nonbonded pdb=" N GLN B 413 " pdb=" OE1 GLN B 413 " model vdw 2.078 2.520 nonbonded pdb=" N GLN A 413 " pdb=" OE1 GLN A 413 " model vdw 2.079 2.520 nonbonded pdb=" N GLN C 413 " pdb=" OE1 GLN C 413 " model vdw 2.079 2.520 nonbonded pdb=" O SER A 331 " pdb=" OG SER A 331 " model vdw 2.339 2.440 nonbonded pdb=" O SER B 331 " pdb=" OG SER B 331 " model vdw 2.339 2.440 ... (remaining 77378 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: 0.990 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: 5.470 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 28.600 Find NCS groups from input model: 0.590 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:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 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 : 0.009 0.075 9534 Z= 0.585 Angle : 0.960 9.435 12936 Z= 0.513 Chirality : 0.056 0.193 1644 Planarity : 0.007 0.073 1572 Dihedral : 13.682 83.912 3426 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % 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: -6.46 (0.14), residues: 1215 helix: -4.23 (0.07), residues: 975 sheet: -2.87 (0.80), residues: 54 loop : -2.72 (0.35), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 276 HIS 0.003 0.001 HIS B 41 PHE 0.021 0.003 PHE B 341 TYR 0.020 0.003 TYR C 373 ARG 0.006 0.001 ARG B 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.133 Fit side-chains REVERT: A 93 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7933 (mtm-85) REVERT: A 200 TYR cc_start: 0.8079 (m-80) cc_final: 0.7821 (m-80) REVERT: A 322 GLN cc_start: 0.8018 (tp40) cc_final: 0.7739 (mm-40) REVERT: A 352 LYS cc_start: 0.8364 (tmtm) cc_final: 0.7721 (mtmt) REVERT: A 393 GLN cc_start: 0.8605 (mt0) cc_final: 0.8184 (mt0) REVERT: B 200 TYR cc_start: 0.8220 (m-80) cc_final: 0.7731 (m-10) REVERT: B 248 MET cc_start: 0.8289 (tpp) cc_final: 0.8083 (tpt) REVERT: B 280 ARG cc_start: 0.8040 (ttp80) cc_final: 0.7807 (tmm160) REVERT: C 200 TYR cc_start: 0.8208 (m-80) cc_final: 0.7746 (m-10) REVERT: C 248 MET cc_start: 0.8260 (tpp) cc_final: 0.8023 (mmt) REVERT: C 316 PHE cc_start: 0.8052 (t80) cc_final: 0.7805 (t80) REVERT: C 322 GLN cc_start: 0.8040 (tp40) cc_final: 0.7667 (mm110) outliers start: 0 outliers final: 2 residues processed: 200 average time/residue: 1.2525 time to fit residues: 267.0176 Evaluate side-chains 148 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain C residue 461 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.7980 chunk 93 optimal weight: 0.0870 chunk 51 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 0.0020 chunk 49 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 37 optimal weight: 0.0170 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.3004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 85 ASN C 85 ASN C 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9534 Z= 0.143 Angle : 0.539 8.061 12936 Z= 0.280 Chirality : 0.037 0.130 1644 Planarity : 0.005 0.036 1572 Dihedral : 4.460 17.648 1297 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.64 % Allowed : 10.05 % Favored : 88.31 % 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: -2.86 (0.20), residues: 1215 helix: -1.52 (0.14), residues: 960 sheet: -2.88 (0.71), residues: 54 loop : -2.33 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 441 HIS 0.001 0.000 HIS B 296 PHE 0.014 0.001 PHE B 357 TYR 0.009 0.001 TYR B 373 ARG 0.004 0.001 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 184 time to evaluate : 1.113 Fit side-chains REVERT: A 205 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.6423 (tmm) REVERT: A 248 MET cc_start: 0.8055 (tpt) cc_final: 0.7665 (mmt) REVERT: A 322 GLN cc_start: 0.7853 (tp40) cc_final: 0.7543 (mm-40) REVERT: B 200 TYR cc_start: 0.8030 (m-80) cc_final: 0.7623 (m-10) REVERT: B 473 MET cc_start: 0.7140 (ttt) cc_final: 0.6844 (mtp) REVERT: C 248 MET cc_start: 0.7994 (tpp) cc_final: 0.7578 (mmt) REVERT: C 280 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7074 (ttm170) REVERT: C 322 GLN cc_start: 0.7812 (tp40) cc_final: 0.7446 (mm-40) REVERT: C 393 GLN cc_start: 0.8591 (mt0) cc_final: 0.8358 (mt0) outliers start: 17 outliers final: 5 residues processed: 192 average time/residue: 1.0192 time to fit residues: 211.7570 Evaluate side-chains 149 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 142 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 388 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 156 GLN B 85 ASN B 156 GLN B 312 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9534 Z= 0.167 Angle : 0.512 6.863 12936 Z= 0.263 Chirality : 0.038 0.125 1644 Planarity : 0.004 0.030 1572 Dihedral : 4.027 17.553 1293 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.80 % Allowed : 14.01 % Favored : 83.19 % 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: -0.78 (0.24), residues: 1215 helix: 0.03 (0.16), residues: 948 sheet: -2.31 (0.75), residues: 54 loop : -1.96 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 441 HIS 0.000 0.000 HIS C 296 PHE 0.014 0.001 PHE A 218 TYR 0.009 0.001 TYR A 373 ARG 0.004 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 1.095 Fit side-chains REVERT: A 205 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.6373 (tmm) REVERT: A 248 MET cc_start: 0.8100 (tpt) cc_final: 0.7783 (mmp) REVERT: A 393 GLN cc_start: 0.8493 (mt0) cc_final: 0.8118 (mt0) REVERT: B 200 TYR cc_start: 0.8064 (m-80) cc_final: 0.7664 (m-10) REVERT: B 473 MET cc_start: 0.7164 (ttt) cc_final: 0.6866 (mtp) REVERT: C 248 MET cc_start: 0.8036 (tpp) cc_final: 0.7570 (mmt) REVERT: C 280 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7098 (ttm170) REVERT: C 322 GLN cc_start: 0.7825 (tp40) cc_final: 0.7453 (mm-40) REVERT: C 393 GLN cc_start: 0.8576 (mt0) cc_final: 0.8261 (mt0) outliers start: 29 outliers final: 12 residues processed: 167 average time/residue: 1.1742 time to fit residues: 210.0947 Evaluate side-chains 153 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 355 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 0.0170 chunk 112 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 32 optimal weight: 0.0000 chunk 99 optimal weight: 0.5980 overall best weight: 0.6624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 85 ASN C 85 ASN C 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9534 Z= 0.146 Angle : 0.486 6.332 12936 Z= 0.249 Chirality : 0.037 0.124 1644 Planarity : 0.003 0.031 1572 Dihedral : 3.833 17.172 1293 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.29 % Allowed : 14.78 % Favored : 81.93 % 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 (0.25), residues: 1215 helix: 0.86 (0.17), residues: 933 sheet: -2.04 (0.80), residues: 54 loop : -1.32 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 441 HIS 0.001 0.000 HIS A 41 PHE 0.015 0.001 PHE C 316 TYR 0.010 0.001 TYR A 373 ARG 0.003 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 159 time to evaluate : 1.055 Fit side-chains REVERT: A 220 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8654 (tp) REVERT: A 248 MET cc_start: 0.8054 (tpt) cc_final: 0.7791 (mmp) REVERT: A 393 GLN cc_start: 0.8505 (mt0) cc_final: 0.8138 (mt0) REVERT: B 75 MET cc_start: 0.8486 (mmm) cc_final: 0.8186 (tpp) REVERT: B 200 TYR cc_start: 0.8100 (m-80) cc_final: 0.7737 (m-10) REVERT: B 303 LEU cc_start: 0.8323 (tp) cc_final: 0.7963 (tt) REVERT: B 473 MET cc_start: 0.7165 (ttt) cc_final: 0.6867 (mtp) REVERT: C 248 MET cc_start: 0.8036 (tpp) cc_final: 0.7765 (mmt) REVERT: C 280 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7075 (ttm170) REVERT: C 303 LEU cc_start: 0.8332 (tp) cc_final: 0.8005 (tt) REVERT: C 322 GLN cc_start: 0.7823 (tp40) cc_final: 0.7325 (mm-40) REVERT: C 342 ARG cc_start: 0.7499 (ppt170) cc_final: 0.7215 (ppt90) REVERT: C 393 GLN cc_start: 0.8556 (mt0) cc_final: 0.8223 (mt0) REVERT: C 463 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7422 (tm-30) outliers start: 34 outliers final: 14 residues processed: 179 average time/residue: 1.0559 time to fit residues: 203.7423 Evaluate side-chains 156 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 463 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 82 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 85 ASN B 366 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9534 Z= 0.195 Angle : 0.512 6.044 12936 Z= 0.261 Chirality : 0.038 0.123 1644 Planarity : 0.003 0.030 1572 Dihedral : 3.865 17.199 1293 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.06 % Allowed : 14.78 % Favored : 81.16 % 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: 0.55 (0.25), residues: 1215 helix: 0.96 (0.17), residues: 972 sheet: -2.01 (0.78), residues: 54 loop : -1.67 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 19 HIS 0.001 0.000 HIS C 296 PHE 0.014 0.001 PHE B 218 TYR 0.009 0.001 TYR A 373 ARG 0.003 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 149 time to evaluate : 1.139 Fit side-chains REVERT: A 220 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8672 (tp) REVERT: A 248 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7889 (mmp) REVERT: A 393 GLN cc_start: 0.8525 (mt0) cc_final: 0.8108 (mt0) REVERT: A 463 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7225 (tt0) REVERT: B 75 MET cc_start: 0.8496 (mmm) cc_final: 0.8201 (tpp) REVERT: B 200 TYR cc_start: 0.8127 (m-80) cc_final: 0.7753 (m-10) REVERT: B 303 LEU cc_start: 0.8337 (tp) cc_final: 0.7959 (tt) REVERT: B 473 MET cc_start: 0.7108 (ttt) cc_final: 0.6825 (mtp) REVERT: C 248 MET cc_start: 0.8087 (tpp) cc_final: 0.7653 (mmt) REVERT: C 280 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7095 (ttm170) REVERT: C 303 LEU cc_start: 0.8339 (tp) cc_final: 0.8002 (tt) REVERT: C 322 GLN cc_start: 0.7816 (tp40) cc_final: 0.7364 (mm-40) REVERT: C 463 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7471 (tm-30) outliers start: 42 outliers final: 20 residues processed: 172 average time/residue: 1.0700 time to fit residues: 198.6771 Evaluate side-chains 162 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 463 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN C 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9534 Z= 0.296 Angle : 0.563 5.979 12936 Z= 0.287 Chirality : 0.041 0.129 1644 Planarity : 0.004 0.040 1572 Dihedral : 4.101 16.422 1293 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.86 % Allowed : 16.14 % Favored : 80.00 % 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: 0.52 (0.25), residues: 1215 helix: 1.01 (0.17), residues: 963 sheet: -1.94 (0.78), residues: 54 loop : -2.01 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 276 HIS 0.002 0.001 HIS B 41 PHE 0.016 0.002 PHE C 316 TYR 0.009 0.001 TYR A 373 ARG 0.003 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 148 time to evaluate : 1.103 Fit side-chains REVERT: A 220 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8685 (tp) REVERT: A 393 GLN cc_start: 0.8546 (mt0) cc_final: 0.8127 (mt0) REVERT: B 200 TYR cc_start: 0.8159 (m-80) cc_final: 0.7789 (m-10) REVERT: B 342 ARG cc_start: 0.7673 (ppt170) cc_final: 0.7379 (ppt90) REVERT: B 473 MET cc_start: 0.7105 (ttt) cc_final: 0.6825 (mtp) REVERT: C 248 MET cc_start: 0.8121 (tpp) cc_final: 0.7651 (mmt) REVERT: C 280 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7036 (ttm110) REVERT: C 320 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7498 (mmt) REVERT: C 322 GLN cc_start: 0.7822 (tp40) cc_final: 0.7444 (mm-40) REVERT: C 463 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7474 (tm-30) outliers start: 40 outliers final: 20 residues processed: 168 average time/residue: 1.1228 time to fit residues: 203.0080 Evaluate side-chains 166 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 463 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 118 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN C 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9534 Z= 0.186 Angle : 0.505 5.554 12936 Z= 0.259 Chirality : 0.038 0.127 1644 Planarity : 0.003 0.049 1572 Dihedral : 3.901 16.651 1293 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.19 % Allowed : 17.97 % Favored : 78.84 % 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: 0.96 (0.25), residues: 1215 helix: 1.36 (0.17), residues: 957 sheet: -2.03 (0.76), residues: 54 loop : -1.93 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 276 HIS 0.001 0.000 HIS A 41 PHE 0.013 0.001 PHE A 218 TYR 0.012 0.001 TYR C 373 ARG 0.002 0.000 ARG B 445 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 149 time to evaluate : 1.054 Fit side-chains REVERT: A 220 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8672 (tp) REVERT: A 393 GLN cc_start: 0.8510 (mt0) cc_final: 0.8098 (mt0) REVERT: A 463 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7231 (tt0) REVERT: B 75 MET cc_start: 0.8532 (mmm) cc_final: 0.8235 (tpp) REVERT: B 200 TYR cc_start: 0.8105 (m-80) cc_final: 0.7742 (m-10) REVERT: B 320 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7592 (mmt) REVERT: B 322 GLN cc_start: 0.7887 (tp40) cc_final: 0.7396 (mm-40) REVERT: B 342 ARG cc_start: 0.7660 (ppt170) cc_final: 0.7364 (ppt90) REVERT: B 463 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7341 (tm-30) REVERT: B 473 MET cc_start: 0.7105 (mtt) cc_final: 0.6822 (mtp) REVERT: C 248 MET cc_start: 0.8091 (tpp) cc_final: 0.7655 (mmt) REVERT: C 280 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7077 (ttm170) REVERT: C 322 GLN cc_start: 0.7760 (tp40) cc_final: 0.7397 (mm-40) REVERT: C 463 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7499 (tm-30) outliers start: 33 outliers final: 19 residues processed: 165 average time/residue: 1.1445 time to fit residues: 202.2025 Evaluate side-chains 172 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 463 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 75 optimal weight: 0.0970 chunk 80 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 93 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 85 ASN C 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9534 Z= 0.136 Angle : 0.484 5.785 12936 Z= 0.248 Chirality : 0.037 0.124 1644 Planarity : 0.003 0.052 1572 Dihedral : 3.672 16.957 1293 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.90 % Allowed : 18.16 % Favored : 78.94 % 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: 1.45 (0.25), residues: 1215 helix: 1.68 (0.18), residues: 963 sheet: -1.93 (0.77), residues: 54 loop : -1.68 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 276 HIS 0.001 0.000 HIS C 296 PHE 0.011 0.001 PHE A 218 TYR 0.014 0.001 TYR C 373 ARG 0.002 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 149 time to evaluate : 1.007 Fit side-chains REVERT: A 393 GLN cc_start: 0.8472 (mt0) cc_final: 0.8060 (mt0) REVERT: A 463 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7216 (tt0) REVERT: B 75 MET cc_start: 0.8492 (mmm) cc_final: 0.8200 (tpp) REVERT: B 200 TYR cc_start: 0.8067 (m-80) cc_final: 0.7692 (m-10) REVERT: B 320 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7527 (mmt) REVERT: B 322 GLN cc_start: 0.7824 (tp40) cc_final: 0.7336 (mm-40) REVERT: B 342 ARG cc_start: 0.7658 (ppt170) cc_final: 0.7367 (ppt90) REVERT: B 473 MET cc_start: 0.7145 (ttt) cc_final: 0.6857 (mtp) REVERT: C 248 MET cc_start: 0.8093 (tpp) cc_final: 0.7800 (mmt) REVERT: C 303 LEU cc_start: 0.8351 (tp) cc_final: 0.8024 (tt) REVERT: C 322 GLN cc_start: 0.7687 (tp40) cc_final: 0.7345 (mm-40) outliers start: 30 outliers final: 19 residues processed: 162 average time/residue: 1.1467 time to fit residues: 199.2795 Evaluate side-chains 163 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 143 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 99 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9534 Z= 0.167 Angle : 0.509 6.178 12936 Z= 0.260 Chirality : 0.038 0.123 1644 Planarity : 0.003 0.052 1572 Dihedral : 3.707 17.225 1293 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.13 % Allowed : 18.94 % Favored : 78.94 % 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: 1.71 (0.26), residues: 1215 helix: 1.84 (0.18), residues: 948 sheet: -1.88 (0.76), residues: 54 loop : -1.18 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 276 HIS 0.001 0.000 HIS A 41 PHE 0.012 0.001 PHE A 218 TYR 0.013 0.001 TYR C 373 ARG 0.002 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 149 time to evaluate : 1.023 Fit side-chains REVERT: A 393 GLN cc_start: 0.8500 (mt0) cc_final: 0.8062 (mt0) REVERT: B 75 MET cc_start: 0.8512 (mmm) cc_final: 0.8229 (tpp) REVERT: B 200 TYR cc_start: 0.8061 (m-80) cc_final: 0.7692 (m-10) REVERT: B 320 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7523 (mmt) REVERT: B 322 GLN cc_start: 0.7809 (tp40) cc_final: 0.7336 (mm-40) REVERT: B 342 ARG cc_start: 0.7660 (ppt170) cc_final: 0.7363 (ppt90) REVERT: B 473 MET cc_start: 0.7144 (ttt) cc_final: 0.6846 (mtp) REVERT: C 248 MET cc_start: 0.8111 (tpp) cc_final: 0.7819 (mmt) REVERT: C 303 LEU cc_start: 0.8343 (tp) cc_final: 0.8015 (tt) REVERT: C 322 GLN cc_start: 0.7610 (tp40) cc_final: 0.7327 (mm-40) outliers start: 22 outliers final: 17 residues processed: 159 average time/residue: 1.1133 time to fit residues: 190.2293 Evaluate side-chains 166 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 0.1980 chunk 122 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 75 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 77 optimal weight: 0.0870 chunk 103 optimal weight: 6.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN C 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9534 Z= 0.144 Angle : 0.506 9.420 12936 Z= 0.255 Chirality : 0.037 0.123 1644 Planarity : 0.003 0.051 1572 Dihedral : 3.653 16.765 1293 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.93 % Allowed : 19.52 % Favored : 78.55 % 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: 1.93 (0.26), residues: 1215 helix: 1.99 (0.18), residues: 948 sheet: -1.86 (0.76), residues: 54 loop : -1.10 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 276 HIS 0.000 0.000 HIS C 296 PHE 0.011 0.001 PHE A 218 TYR 0.013 0.001 TYR C 373 ARG 0.002 0.000 ARG C 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 1.242 Fit side-chains REVERT: A 75 MET cc_start: 0.8519 (mmp) cc_final: 0.8269 (mmp) REVERT: A 393 GLN cc_start: 0.8471 (mt0) cc_final: 0.8047 (mt0) REVERT: A 463 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7160 (tt0) REVERT: B 75 MET cc_start: 0.8496 (mmm) cc_final: 0.8211 (tpp) REVERT: B 200 TYR cc_start: 0.8072 (m-80) cc_final: 0.7708 (m-10) REVERT: B 320 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7442 (mmt) REVERT: B 322 GLN cc_start: 0.7768 (tp40) cc_final: 0.7326 (mm-40) REVERT: B 329 MET cc_start: 0.6495 (mmm) cc_final: 0.6162 (mmt) REVERT: B 342 ARG cc_start: 0.7635 (ppt170) cc_final: 0.7384 (ppt90) REVERT: B 463 GLU cc_start: 0.7540 (tt0) cc_final: 0.7282 (tm-30) REVERT: B 473 MET cc_start: 0.7123 (ttt) cc_final: 0.6823 (mtp) REVERT: C 248 MET cc_start: 0.8092 (tpp) cc_final: 0.7801 (mmt) REVERT: C 303 LEU cc_start: 0.8340 (tp) cc_final: 0.8010 (tt) REVERT: C 322 GLN cc_start: 0.7599 (tp40) cc_final: 0.7350 (mm-40) REVERT: C 463 GLU cc_start: 0.7725 (tp30) cc_final: 0.7394 (tm-30) outliers start: 20 outliers final: 18 residues processed: 156 average time/residue: 1.1493 time to fit residues: 192.4622 Evaluate side-chains 163 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 14 optimal weight: 0.0670 chunk 27 optimal weight: 0.3980 chunk 97 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.140586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.100481 restraints weight = 11198.851| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.83 r_work: 0.2928 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9534 Z= 0.156 Angle : 0.526 8.904 12936 Z= 0.264 Chirality : 0.038 0.121 1644 Planarity : 0.003 0.051 1572 Dihedral : 3.636 16.559 1293 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.22 % Allowed : 19.32 % Favored : 78.45 % 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: 2.00 (0.26), residues: 1215 helix: 2.05 (0.18), residues: 945 sheet: -1.84 (0.76), residues: 54 loop : -1.08 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 276 HIS 0.000 0.000 HIS A 41 PHE 0.011 0.001 PHE A 218 TYR 0.015 0.001 TYR B 373 ARG 0.002 0.000 ARG C 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3776.99 seconds wall clock time: 67 minutes 3.20 seconds (4023.20 seconds total)