Starting phenix.real_space_refine on Sun Aug 4 09:13:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ors_17131/08_2024/8ors_17131.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ors_17131/08_2024/8ors_17131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ors_17131/08_2024/8ors_17131.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ors_17131/08_2024/8ors_17131.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ors_17131/08_2024/8ors_17131.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ors_17131/08_2024/8ors_17131.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 32 5.16 5 C 6434 2.51 5 N 1742 2.21 5 O 1912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 179": "OD1" <-> "OD2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 502": "OD1" <-> "OD2" Residue "B GLU 566": "OE1" <-> "OE2" Residue "B ASP 610": "OD1" <-> "OD2" Residue "B TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10124 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "B" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.97, per 1000 atoms: 0.69 Number of scatterers: 10124 At special positions: 0 Unit cell: (91.2156, 97.731, 111.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 4 15.00 O 1912 8.00 N 1742 7.00 C 6434 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: 4.08 Conformation dependent library (CDL) restraints added in 1.8 seconds 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 17 sheets defined 39.3% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 67 through 79 Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 132 through 136 removed outlier: 3.996A pdb=" N TYR A 136 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 164 through 170 Processing helix chain 'A' and resid 176 through 192 removed outlier: 5.949A pdb=" N ASN A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N TYR A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 221 removed outlier: 3.846A pdb=" N SER A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 299 through 305 removed outlier: 4.439A pdb=" N GLY A 304 " --> pdb=" O LYS A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 361 Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 402 through 410 Processing helix chain 'A' and resid 438 through 443 removed outlier: 4.337A pdb=" N ASN A 442 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 468 Processing helix chain 'A' and resid 520 through 523 removed outlier: 3.596A pdb=" N GLN A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 523' Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'A' and resid 532 through 559 removed outlier: 3.573A pdb=" N ILE A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN A 554 " --> pdb=" O ILE A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 586 Processing helix chain 'A' and resid 587 through 594 removed outlier: 4.606A pdb=" N TRP A 590 " --> pdb=" O ALA A 587 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS A 591 " --> pdb=" O ASN A 588 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 592 " --> pdb=" O TRP A 589 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 594 " --> pdb=" O HIS A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 616 removed outlier: 3.541A pdb=" N SER A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 622 removed outlier: 3.796A pdb=" N ARG A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 667 through 684 removed outlier: 4.073A pdb=" N ALA A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 672 " --> pdb=" O TRP A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 691 Processing helix chain 'B' and resid 67 through 79 Processing helix chain 'B' and resid 95 through 100 removed outlier: 3.504A pdb=" N ASP B 100 " --> pdb=" O PRO B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 149 through 154 Processing helix chain 'B' and resid 164 through 170 Processing helix chain 'B' and resid 176 through 192 removed outlier: 5.873A pdb=" N ASN B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N TYR B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 221 removed outlier: 3.935A pdb=" N SER B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 Processing helix chain 'B' and resid 299 through 303 Processing helix chain 'B' and resid 352 through 361 Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 402 through 410 Processing helix chain 'B' and resid 438 through 443 removed outlier: 4.107A pdb=" N ASN B 442 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 468 Processing helix chain 'B' and resid 520 through 532 Proline residue: B 526 - end of helix Processing helix chain 'B' and resid 532 through 559 removed outlier: 3.953A pdb=" N GLN B 554 " --> pdb=" O ILE B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 586 removed outlier: 3.670A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 593 removed outlier: 4.351A pdb=" N TRP B 590 " --> pdb=" O ALA B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 599 removed outlier: 3.611A pdb=" N VAL B 598 " --> pdb=" O VAL B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 616 Processing helix chain 'B' and resid 616 through 622 removed outlier: 4.247A pdb=" N ARG B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 621 " --> pdb=" O TYR B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 659 Processing helix chain 'B' and resid 668 through 684 Processing helix chain 'B' and resid 686 through 691 Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 308 removed outlier: 6.272A pdb=" N ILE A 83 " --> pdb=" O ARG A 306 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL A 308 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 85 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N THR A 56 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 9.857A pdb=" N LYS A 342 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ASP A 58 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL A 344 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL A 60 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL A 346 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 62 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 328 " --> pdb=" O HIS A 336 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLY A 325 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILE A 316 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASN A 327 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 306 through 308 removed outlier: 6.272A pdb=" N ILE A 83 " --> pdb=" O ARG A 306 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL A 308 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 85 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N THR A 56 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 9.857A pdb=" N LYS A 342 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ASP A 58 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL A 344 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL A 60 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL A 346 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 62 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 124 through 128 removed outlier: 3.577A pdb=" N HIS A 144 " --> pdb=" O TRP A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.546A pdb=" N VAL A 260 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA A 426 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLN A 450 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 428 " --> pdb=" O LYS A 448 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 481 " --> pdb=" O PRO A 393 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.546A pdb=" N VAL A 260 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA A 426 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLN A 450 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 428 " --> pdb=" O LYS A 448 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 481 " --> pdb=" O PRO A 393 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 392 " --> pdb=" O HIS A 624 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA7, first strand: chain 'A' and resid 362 through 363 Processing sheet with id=AA8, first strand: chain 'A' and resid 385 through 387 removed outlier: 5.713A pdb=" N GLY A 490 " --> pdb=" O GLY A 386 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 305 through 308 removed outlier: 6.427A pdb=" N ILE B 83 " --> pdb=" O ARG B 306 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N VAL B 308 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 85 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE B 59 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU B 86 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE B 61 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL B 60 " --> pdb=" O GLU B 343 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 124 through 128 removed outlier: 3.506A pdb=" N HIS B 144 " --> pdb=" O TRP B 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 158 through 159 removed outlier: 4.424A pdb=" N TYR B 266 " --> pdb=" O LEU B 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 269 through 271 Processing sheet with id=AB4, first strand: chain 'B' and resid 312 through 318 removed outlier: 3.528A pdb=" N ASP B 314 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ASN B 327 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE B 316 " --> pdb=" O GLY B 325 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLY B 325 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE B 318 " --> pdb=" O ALA B 323 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA B 323 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 338 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR B 328 " --> pdb=" O HIS B 336 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS B 336 " --> pdb=" O TYR B 328 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 362 through 363 Processing sheet with id=AB6, first strand: chain 'B' and resid 385 through 387 removed outlier: 5.508A pdb=" N THR B 385 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE B 492 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 449 through 455 removed outlier: 3.608A pdb=" N THR B 478 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 481 " --> pdb=" O PRO B 393 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 564 " --> pdb=" O HIS B 400 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 449 through 455 removed outlier: 3.608A pdb=" N THR B 478 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 481 " --> pdb=" O PRO B 393 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.33 Time building geometry restraints manager: 4.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3334 1.34 - 1.46: 2113 1.46 - 1.57: 4868 1.57 - 1.69: 5 1.69 - 1.81: 60 Bond restraints: 10380 Sorted by residual: bond pdb=" O3P FAD A 901 " pdb=" P FAD A 901 " ideal model delta sigma weight residual 1.660 1.584 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" O3P FAD B 901 " pdb=" P FAD B 901 " ideal model delta sigma weight residual 1.660 1.584 0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" O5' FAD B 901 " pdb=" P FAD B 901 " ideal model delta sigma weight residual 1.637 1.573 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O5' FAD A 901 " pdb=" P FAD A 901 " ideal model delta sigma weight residual 1.637 1.574 0.063 2.00e-02 2.50e+03 9.88e+00 bond pdb=" O5B FAD B 901 " pdb=" PA FAD B 901 " ideal model delta sigma weight residual 1.634 1.572 0.062 2.00e-02 2.50e+03 9.70e+00 ... (remaining 10375 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.10: 397 107.10 - 113.84: 5689 113.84 - 120.58: 4038 120.58 - 127.32: 3925 127.32 - 134.07: 129 Bond angle restraints: 14178 Sorted by residual: angle pdb=" N VAL B 324 " pdb=" CA VAL B 324 " pdb=" C VAL B 324 " ideal model delta sigma weight residual 113.43 109.58 3.85 1.09e+00 8.42e-01 1.25e+01 angle pdb=" CA GLY B 325 " pdb=" C GLY B 325 " pdb=" O GLY B 325 " ideal model delta sigma weight residual 121.62 118.25 3.37 9.80e-01 1.04e+00 1.18e+01 angle pdb=" N GLY A 401 " pdb=" CA GLY A 401 " pdb=" C GLY A 401 " ideal model delta sigma weight residual 110.56 115.00 -4.44 1.36e+00 5.41e-01 1.07e+01 angle pdb=" O1P FAD A 901 " pdb=" P FAD A 901 " pdb=" O2P FAD A 901 " ideal model delta sigma weight residual 122.50 114.68 7.82 3.00e+00 1.11e-01 6.79e+00 angle pdb=" O1P FAD B 901 " pdb=" P FAD B 901 " pdb=" O2P FAD B 901 " ideal model delta sigma weight residual 122.50 115.14 7.36 3.00e+00 1.11e-01 6.03e+00 ... (remaining 14173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.27: 5844 24.27 - 48.55: 265 48.55 - 72.82: 28 72.82 - 97.10: 8 97.10 - 121.37: 1 Dihedral angle restraints: 6146 sinusoidal: 2426 harmonic: 3720 Sorted by residual: dihedral pdb=" O5' FAD B 901 " pdb=" O3P FAD B 901 " pdb=" P FAD B 901 " pdb=" PA FAD B 901 " ideal model delta sinusoidal sigma weight residual 298.23 176.86 121.37 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" CA ASN B 666 " pdb=" C ASN B 666 " pdb=" N THR B 667 " pdb=" CA THR B 667 " ideal model delta harmonic sigma weight residual -180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ASN A 666 " pdb=" C ASN A 666 " pdb=" N THR A 667 " pdb=" CA THR A 667 " ideal model delta harmonic sigma weight residual -180.00 -161.45 -18.55 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 6143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 975 0.033 - 0.065: 370 0.065 - 0.098: 137 0.098 - 0.131: 84 0.131 - 0.163: 6 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CA ILE B 459 " pdb=" N ILE B 459 " pdb=" C ILE B 459 " pdb=" CB ILE B 459 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.66e-01 chirality pdb=" C2B FAD A 901 " pdb=" C1B FAD A 901 " pdb=" C3B FAD A 901 " pdb=" O2B FAD A 901 " both_signs ideal model delta sigma weight residual False -2.53 -2.68 0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE A 459 " pdb=" N ILE A 459 " pdb=" C ILE A 459 " pdb=" CB ILE A 459 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 1569 not shown) Planarity restraints: 1844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 569 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO B 570 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 570 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 570 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 569 " 0.027 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 570 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 570 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 570 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 602 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO B 603 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 603 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 603 " 0.018 5.00e-02 4.00e+02 ... (remaining 1841 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 194 2.68 - 3.23: 9739 3.23 - 3.79: 15397 3.79 - 4.34: 21018 4.34 - 4.90: 35262 Nonbonded interactions: 81610 Sorted by model distance: nonbonded pdb=" OD1 ASN B 416 " pdb=" OG1 THR B 418 " model vdw 2.121 3.040 nonbonded pdb=" O GLY B 149 " pdb=" OG1 THR B 152 " model vdw 2.160 3.040 nonbonded pdb=" O GLY A 349 " pdb=" OG1 THR A 353 " model vdw 2.188 3.040 nonbonded pdb=" O GLY A 149 " pdb=" OG1 THR A 152 " model vdw 2.209 3.040 nonbonded pdb=" NZ LYS B 644 " pdb=" O GLN B 649 " model vdw 2.253 3.120 ... (remaining 81605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.260 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 33.240 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 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 : 0.003 0.076 10380 Z= 0.220 Angle : 0.551 7.815 14178 Z= 0.280 Chirality : 0.045 0.163 1572 Planarity : 0.004 0.044 1844 Dihedral : 13.613 121.372 3786 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.02 (0.24), residues: 1294 helix: 1.08 (0.27), residues: 394 sheet: -0.35 (0.40), residues: 190 loop : -0.44 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 125 HIS 0.002 0.000 HIS B 92 PHE 0.014 0.001 PHE A 365 TYR 0.007 0.001 TYR B 74 ARG 0.002 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.575 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.2490 time to fit residues: 19.2894 Evaluate side-chains 37 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 HIS B 547 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10380 Z= 0.219 Angle : 0.576 9.401 14178 Z= 0.294 Chirality : 0.047 0.160 1572 Planarity : 0.005 0.043 1844 Dihedral : 7.691 106.669 1514 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % 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: -0.10 (0.24), residues: 1294 helix: 1.09 (0.27), residues: 400 sheet: -0.34 (0.37), residues: 220 loop : -0.64 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 125 HIS 0.003 0.001 HIS B 390 PHE 0.013 0.001 PHE B 486 TYR 0.013 0.001 TYR A 491 ARG 0.002 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.185 Fit side-chains REVERT: B 179 ASP cc_start: 0.6458 (t0) cc_final: 0.6231 (t0) REVERT: B 402 GLU cc_start: 0.8358 (mp0) cc_final: 0.8079 (mp0) REVERT: B 566 GLU cc_start: 0.5875 (tp30) cc_final: 0.5635 (pt0) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1945 time to fit residues: 14.9755 Evaluate side-chains 39 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 79 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN B 138 ASN B 379 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 10380 Z= 0.288 Angle : 0.612 11.430 14178 Z= 0.309 Chirality : 0.048 0.169 1572 Planarity : 0.005 0.043 1844 Dihedral : 7.255 105.504 1514 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.09 % Allowed : 3.33 % Favored : 96.58 % 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: -0.32 (0.24), residues: 1294 helix: 0.93 (0.26), residues: 400 sheet: -0.59 (0.36), residues: 220 loop : -0.73 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 125 HIS 0.003 0.001 HIS A 144 PHE 0.021 0.002 PHE A 486 TYR 0.013 0.001 TYR A 367 ARG 0.008 0.001 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 1.189 Fit side-chains REVERT: B 179 ASP cc_start: 0.6536 (t0) cc_final: 0.6210 (t0) REVERT: B 402 GLU cc_start: 0.8345 (mp0) cc_final: 0.8062 (mp0) REVERT: B 420 MET cc_start: 0.8867 (mmm) cc_final: 0.8641 (mmt) outliers start: 1 outliers final: 0 residues processed: 50 average time/residue: 0.2048 time to fit residues: 16.3912 Evaluate side-chains 37 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- 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: 0.7566 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10380 Z= 0.276 Angle : 0.611 11.649 14178 Z= 0.308 Chirality : 0.048 0.170 1572 Planarity : 0.005 0.043 1844 Dihedral : 6.838 102.226 1514 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % 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: -0.44 (0.24), residues: 1294 helix: 0.88 (0.26), residues: 400 sheet: -0.83 (0.36), residues: 222 loop : -0.77 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 125 HIS 0.003 0.001 HIS B 390 PHE 0.024 0.002 PHE A 486 TYR 0.013 0.001 TYR A 491 ARG 0.004 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.190 Fit side-chains REVERT: B 146 MET cc_start: 0.6744 (mtp) cc_final: 0.6414 (mtp) REVERT: B 179 ASP cc_start: 0.6564 (t0) cc_final: 0.6241 (t0) REVERT: B 420 MET cc_start: 0.8865 (mmm) cc_final: 0.8503 (mmt) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2232 time to fit residues: 15.9269 Evaluate side-chains 35 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 1 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 63 optimal weight: 6.9990 chunk 111 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 562 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10380 Z= 0.289 Angle : 0.620 12.185 14178 Z= 0.312 Chirality : 0.048 0.168 1572 Planarity : 0.005 0.044 1844 Dihedral : 6.804 102.316 1514 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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: -0.54 (0.24), residues: 1294 helix: 0.85 (0.26), residues: 400 sheet: -0.96 (0.36), residues: 222 loop : -0.84 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 125 HIS 0.003 0.001 HIS A 144 PHE 0.020 0.002 PHE B 365 TYR 0.014 0.001 TYR A 491 ARG 0.003 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 2.201 Fit side-chains REVERT: A 75 LEU cc_start: 0.8778 (mt) cc_final: 0.8576 (mp) REVERT: B 179 ASP cc_start: 0.6590 (t0) cc_final: 0.6258 (t0) REVERT: B 420 MET cc_start: 0.8860 (mmm) cc_final: 0.8509 (mmt) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2143 time to fit residues: 15.9367 Evaluate side-chains 36 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 24 optimal weight: 0.0370 chunk 72 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 overall best weight: 4.4066 ------------------------------------------------------------------------------- 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: 0.7558 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10380 Z= 0.234 Angle : 0.589 11.544 14178 Z= 0.296 Chirality : 0.047 0.161 1572 Planarity : 0.005 0.042 1844 Dihedral : 6.714 103.392 1514 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: -0.48 (0.24), residues: 1294 helix: 0.91 (0.26), residues: 400 sheet: -0.87 (0.36), residues: 220 loop : -0.83 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 125 HIS 0.002 0.001 HIS A 144 PHE 0.015 0.001 PHE A 477 TYR 0.012 0.001 TYR A 491 ARG 0.003 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.133 Fit side-chains REVERT: B 420 MET cc_start: 0.8854 (mmm) cc_final: 0.8492 (mmt) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2128 time to fit residues: 15.1878 Evaluate side-chains 37 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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: 0.7554 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10380 Z= 0.234 Angle : 0.597 11.435 14178 Z= 0.299 Chirality : 0.047 0.157 1572 Planarity : 0.005 0.043 1844 Dihedral : 6.689 104.654 1514 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: -0.48 (0.24), residues: 1294 helix: 0.91 (0.26), residues: 400 sheet: -0.91 (0.36), residues: 222 loop : -0.82 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.004 0.001 HIS A 591 PHE 0.018 0.002 PHE A 593 TYR 0.012 0.001 TYR A 491 ARG 0.003 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.238 Fit side-chains REVERT: B 420 MET cc_start: 0.8860 (mmm) cc_final: 0.8533 (mmt) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1983 time to fit residues: 15.7459 Evaluate side-chains 34 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.7541 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10380 Z= 0.203 Angle : 0.580 10.772 14178 Z= 0.290 Chirality : 0.047 0.153 1572 Planarity : 0.005 0.044 1844 Dihedral : 6.620 106.099 1514 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 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: -0.42 (0.24), residues: 1294 helix: 0.96 (0.26), residues: 400 sheet: -0.82 (0.37), residues: 220 loop : -0.81 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 125 HIS 0.002 0.001 HIS B 92 PHE 0.015 0.001 PHE A 477 TYR 0.010 0.001 TYR A 491 ARG 0.003 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.150 Fit side-chains REVERT: B 420 MET cc_start: 0.8875 (mmm) cc_final: 0.8542 (mmt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2022 time to fit residues: 15.4744 Evaluate side-chains 38 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 69 optimal weight: 0.1980 chunk 50 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 108 optimal weight: 0.0980 chunk 75 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 overall best weight: 4.2586 ------------------------------------------------------------------------------- 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: 0.7548 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10380 Z= 0.229 Angle : 0.590 11.246 14178 Z= 0.295 Chirality : 0.048 0.207 1572 Planarity : 0.005 0.045 1844 Dihedral : 6.621 106.973 1514 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 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: -0.48 (0.24), residues: 1294 helix: 0.92 (0.26), residues: 400 sheet: -0.93 (0.36), residues: 222 loop : -0.81 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 125 HIS 0.003 0.001 HIS A 144 PHE 0.014 0.001 PHE A 477 TYR 0.015 0.001 TYR B 177 ARG 0.003 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.243 Fit side-chains REVERT: B 420 MET cc_start: 0.8877 (mmm) cc_final: 0.8539 (mmt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1992 time to fit residues: 15.3509 Evaluate side-chains 36 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.2184 > 50: distance: 57 - 71: 29.717 distance: 61 - 79: 14.623 distance: 66 - 71: 27.816 distance: 71 - 72: 25.034 distance: 72 - 73: 15.297 distance: 72 - 75: 24.323 distance: 73 - 74: 7.074 distance: 73 - 79: 25.249 distance: 75 - 76: 4.038 distance: 76 - 77: 32.366 distance: 77 - 78: 20.168 distance: 79 - 80: 24.134 distance: 80 - 81: 28.047 distance: 80 - 83: 14.660 distance: 81 - 82: 21.233 distance: 81 - 87: 22.029 distance: 83 - 84: 27.263 distance: 83 - 85: 22.466 distance: 84 - 86: 38.974 distance: 87 - 88: 8.067 distance: 88 - 89: 33.964 distance: 88 - 91: 7.545 distance: 89 - 90: 30.999 distance: 89 - 95: 23.385 distance: 91 - 92: 10.152 distance: 92 - 93: 9.698 distance: 92 - 94: 10.288 distance: 95 - 96: 22.216 distance: 96 - 97: 22.743 distance: 96 - 99: 32.151 distance: 97 - 98: 34.242 distance: 97 - 106: 22.234 distance: 99 - 100: 17.484 distance: 100 - 101: 25.492 distance: 101 - 102: 26.275 distance: 102 - 103: 17.697 distance: 103 - 104: 17.430 distance: 103 - 105: 40.168 distance: 106 - 107: 23.642 distance: 107 - 108: 39.625 distance: 107 - 110: 9.350 distance: 108 - 109: 35.381 distance: 108 - 114: 60.218 distance: 110 - 111: 29.947 distance: 111 - 112: 31.654 distance: 111 - 113: 26.678 distance: 114 - 115: 25.415 distance: 115 - 116: 20.103 distance: 115 - 118: 25.527 distance: 116 - 117: 18.121 distance: 116 - 122: 28.108 distance: 118 - 119: 20.182 distance: 119 - 120: 34.256 distance: 119 - 121: 19.559 distance: 122 - 123: 6.868 distance: 122 - 191: 13.294 distance: 123 - 124: 11.227 distance: 123 - 126: 13.202 distance: 124 - 125: 37.710 distance: 124 - 130: 4.825 distance: 126 - 127: 25.957 distance: 127 - 128: 8.511 distance: 127 - 129: 26.316 distance: 130 - 131: 11.977 distance: 131 - 132: 37.715 distance: 131 - 134: 18.959 distance: 132 - 133: 29.022 distance: 132 - 137: 33.933 distance: 134 - 135: 24.710 distance: 134 - 136: 38.439 distance: 137 - 138: 22.942 distance: 138 - 139: 14.884 distance: 138 - 141: 21.942 distance: 139 - 140: 33.034 distance: 139 - 144: 17.843 distance: 141 - 142: 32.410 distance: 141 - 143: 38.973 distance: 144 - 145: 21.968 distance: 145 - 146: 23.285 distance: 146 - 147: 19.529 distance: 146 - 148: 8.343