Starting phenix.real_space_refine on Sun Aug 4 01:56:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvu_4657/08_2024/6qvu_4657.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvu_4657/08_2024/6qvu_4657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvu_4657/08_2024/6qvu_4657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvu_4657/08_2024/6qvu_4657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvu_4657/08_2024/6qvu_4657.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvu_4657/08_2024/6qvu_4657.cif" } resolution = 4.2 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= 0.003 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: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 6132 2.51 5 N 1484 2.21 5 O 1586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 199": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 626": "NH1" <-> "NH2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B ARG 858": "NH1" <-> "NH2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 626": "NH1" <-> "NH2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 858": "NH1" <-> "NH2" 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: 9272 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4636 Classifications: {'peptide': 599} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 569} Chain breaks: 3 Chain: "A" Number of atoms: 4636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4636 Classifications: {'peptide': 599} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 569} Chain breaks: 3 Time building chain proxies: 5.60, per 1000 atoms: 0.60 Number of scatterers: 9272 At special positions: 0 Unit cell: (105.93, 102.72, 109.14, 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 70 16.00 O 1586 8.00 N 1484 7.00 C 6132 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: 3.92 Conformation dependent library (CDL) restraints added in 1.7 seconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2216 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 6 sheets defined 64.7% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'B' and resid 115 through 153 Processing helix chain 'B' and resid 156 through 181 removed outlier: 3.522A pdb=" N PHE B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 191 through 198 Processing helix chain 'B' and resid 208 through 224 removed outlier: 3.514A pdb=" N ALA B 214 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B 217 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 250 Processing helix chain 'B' and resid 263 through 279 Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 298 through 323 removed outlier: 3.673A pdb=" N TYR B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 319 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 377 removed outlier: 3.912A pdb=" N ALA B 353 " --> pdb=" O PRO B 349 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS B 357 " --> pdb=" O ALA B 353 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N CYS B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY B 375 " --> pdb=" O GLN B 371 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG B 377 " --> pdb=" O MET B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 389 Processing helix chain 'B' and resid 392 through 403 removed outlier: 3.591A pdb=" N ILE B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL B 397 " --> pdb=" O TYR B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 428 Processing helix chain 'B' and resid 444 through 450 removed outlier: 3.804A pdb=" N ILE B 450 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 477 removed outlier: 3.804A pdb=" N ILE B 472 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL B 473 " --> pdb=" O TRP B 469 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET B 477 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 506 Processing helix chain 'B' and resid 521 through 538 removed outlier: 5.213A pdb=" N THR B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 551 removed outlier: 3.620A pdb=" N VAL B 544 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY B 551 " --> pdb=" O PHE B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 574 Processing helix chain 'B' and resid 576 through 586 Processing helix chain 'B' and resid 621 through 632 removed outlier: 3.747A pdb=" N THR B 632 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 666 Processing helix chain 'B' and resid 833 through 845 Processing helix chain 'B' and resid 862 through 872 removed outlier: 4.024A pdb=" N GLY B 872 " --> pdb=" O LYS B 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 153 Processing helix chain 'A' and resid 156 through 181 removed outlier: 3.521A pdb=" N PHE A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 208 through 224 removed outlier: 3.515A pdb=" N ALA A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 217 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 250 Processing helix chain 'A' and resid 263 through 279 Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 298 through 323 removed outlier: 3.673A pdb=" N TYR A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 377 removed outlier: 3.910A pdb=" N ALA A 353 " --> pdb=" O PRO A 349 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A 355 " --> pdb=" O PHE A 351 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N CYS A 358 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY A 375 " --> pdb=" O GLN A 371 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 377 " --> pdb=" O MET A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 389 Processing helix chain 'A' and resid 392 through 403 removed outlier: 3.590A pdb=" N ILE A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL A 397 " --> pdb=" O TYR A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.804A pdb=" N ILE A 450 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 477 removed outlier: 3.803A pdb=" N ILE A 472 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL A 473 " --> pdb=" O TRP A 469 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET A 477 " --> pdb=" O VAL A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 506 Processing helix chain 'A' and resid 521 through 538 removed outlier: 5.213A pdb=" N THR A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 551 removed outlier: 3.620A pdb=" N VAL A 544 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 574 Processing helix chain 'A' and resid 576 through 586 Processing helix chain 'A' and resid 621 through 632 removed outlier: 3.748A pdb=" N THR A 632 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 666 Processing helix chain 'A' and resid 833 through 845 Processing helix chain 'A' and resid 862 through 872 removed outlier: 4.025A pdb=" N GLY A 872 " --> pdb=" O LYS A 868 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 510 through 512 Processing sheet with id=AA2, first strand: chain 'B' and resid 616 through 617 removed outlier: 5.567A pdb=" N VAL B 616 " --> pdb=" O VAL B 640 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LEU B 637 " --> pdb=" O SER B 651 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER B 651 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU B 639 " --> pdb=" O LEU B 649 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 849 through 853 removed outlier: 6.458A pdb=" N ALA B 849 " --> pdb=" O VAL B 860 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL B 860 " --> pdb=" O ALA B 849 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 851 " --> pdb=" O ARG B 858 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 512 Processing sheet with id=AA5, first strand: chain 'A' and resid 616 through 617 removed outlier: 5.567A pdb=" N VAL A 616 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LEU A 637 " --> pdb=" O SER A 651 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER A 651 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU A 639 " --> pdb=" O LEU A 649 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 853 removed outlier: 6.458A pdb=" N ALA A 849 " --> pdb=" O VAL A 860 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL A 860 " --> pdb=" O ALA A 849 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 851 " --> pdb=" O ARG A 858 " (cutoff:3.500A) 551 hydrogen bonds defined for protein. 1617 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: 2.48 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2688 1.34 - 1.46: 1995 1.46 - 1.58: 4705 1.58 - 1.69: 0 1.69 - 1.81: 116 Bond restraints: 9504 Sorted by residual: bond pdb=" C TYR A 393 " pdb=" N PRO A 394 " ideal model delta sigma weight residual 1.336 1.371 -0.035 1.20e-02 6.94e+03 8.31e+00 bond pdb=" C TYR B 393 " pdb=" N PRO B 394 " ideal model delta sigma weight residual 1.336 1.371 -0.035 1.20e-02 6.94e+03 8.31e+00 bond pdb=" CA PHE A 167 " pdb=" C PHE A 167 " ideal model delta sigma weight residual 1.520 1.545 -0.025 1.23e-02 6.61e+03 4.16e+00 bond pdb=" CA PHE B 167 " pdb=" C PHE B 167 " ideal model delta sigma weight residual 1.520 1.545 -0.025 1.23e-02 6.61e+03 4.02e+00 bond pdb=" C LEU A 557 " pdb=" O LEU A 557 " ideal model delta sigma weight residual 1.243 1.262 -0.019 9.50e-03 1.11e+04 3.89e+00 ... (remaining 9499 not shown) Histogram of bond angle deviations from ideal: 97.31 - 104.66: 197 104.66 - 112.02: 4559 112.02 - 119.38: 3344 119.38 - 126.73: 4666 126.73 - 134.09: 148 Bond angle restraints: 12914 Sorted by residual: angle pdb=" C PHE B 343 " pdb=" N ASP B 344 " pdb=" CA ASP B 344 " ideal model delta sigma weight residual 121.70 134.09 -12.39 1.80e+00 3.09e-01 4.74e+01 angle pdb=" C PHE A 343 " pdb=" N ASP A 344 " pdb=" CA ASP A 344 " ideal model delta sigma weight residual 121.70 134.00 -12.30 1.80e+00 3.09e-01 4.67e+01 angle pdb=" C PHE A 468 " pdb=" N TRP A 469 " pdb=" CA TRP A 469 " ideal model delta sigma weight residual 122.56 111.11 11.45 1.72e+00 3.38e-01 4.43e+01 angle pdb=" C PHE B 468 " pdb=" N TRP B 469 " pdb=" CA TRP B 469 " ideal model delta sigma weight residual 122.56 111.12 11.44 1.72e+00 3.38e-01 4.42e+01 angle pdb=" C LYS A 324 " pdb=" N ASP A 325 " pdb=" CA ASP A 325 " ideal model delta sigma weight residual 121.56 129.31 -7.75 1.56e+00 4.11e-01 2.47e+01 ... (remaining 12909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.04: 5000 14.04 - 28.07: 384 28.07 - 42.11: 140 42.11 - 56.15: 18 56.15 - 70.18: 14 Dihedral angle restraints: 5556 sinusoidal: 2114 harmonic: 3442 Sorted by residual: dihedral pdb=" CA VAL B 327 " pdb=" C VAL B 327 " pdb=" N THR B 328 " pdb=" CA THR B 328 " ideal model delta harmonic sigma weight residual -180.00 -119.15 -60.85 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" CA VAL A 327 " pdb=" C VAL A 327 " pdb=" N THR A 328 " pdb=" CA THR A 328 " ideal model delta harmonic sigma weight residual -180.00 -119.18 -60.82 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" CA GLY A 355 " pdb=" C GLY A 355 " pdb=" N ILE A 356 " pdb=" CA ILE A 356 " ideal model delta harmonic sigma weight residual -180.00 -137.60 -42.40 0 5.00e+00 4.00e-02 7.19e+01 ... (remaining 5553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1105 0.063 - 0.126: 342 0.126 - 0.189: 63 0.189 - 0.252: 12 0.252 - 0.315: 4 Chirality restraints: 1526 Sorted by residual: chirality pdb=" CB VAL A 489 " pdb=" CA VAL A 489 " pdb=" CG1 VAL A 489 " pdb=" CG2 VAL A 489 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB VAL B 489 " pdb=" CA VAL B 489 " pdb=" CG1 VAL B 489 " pdb=" CG2 VAL B 489 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CG LEU A 843 " pdb=" CB LEU A 843 " pdb=" CD1 LEU A 843 " pdb=" CD2 LEU A 843 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1523 not shown) Planarity restraints: 1580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 352 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.70e+00 pdb=" C ALA B 352 " 0.048 2.00e-02 2.50e+03 pdb=" O ALA B 352 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA B 353 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 352 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.66e+00 pdb=" C ALA A 352 " -0.048 2.00e-02 2.50e+03 pdb=" O ALA A 352 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA A 353 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 406 " 0.045 5.00e-02 4.00e+02 6.88e-02 7.56e+00 pdb=" N PRO B 407 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 407 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 407 " 0.037 5.00e-02 4.00e+02 ... (remaining 1577 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 736 2.73 - 3.27: 9839 3.27 - 3.82: 16235 3.82 - 4.36: 18375 4.36 - 4.90: 29261 Nonbonded interactions: 74446 Sorted by model distance: nonbonded pdb=" O ILE A 401 " pdb=" OG1 THR A 405 " model vdw 2.191 3.040 nonbonded pdb=" O ILE B 401 " pdb=" OG1 THR B 405 " model vdw 2.192 3.040 nonbonded pdb=" O ILE B 472 " pdb=" OG1 THR B 476 " model vdw 2.255 3.040 nonbonded pdb=" O ILE A 472 " pdb=" OG1 THR A 476 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR B 302 " pdb=" O GLU A 291 " model vdw 2.262 3.040 ... (remaining 74441 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: 1.330 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: 0.100 Process input model: 28.120 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 9504 Z= 0.406 Angle : 1.306 17.027 12914 Z= 0.709 Chirality : 0.064 0.315 1526 Planarity : 0.010 0.069 1580 Dihedral : 12.340 70.183 3340 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 1.99 % Allowed : 9.34 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.71 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.20), residues: 1182 helix: -2.24 (0.15), residues: 770 sheet: -1.63 (1.13), residues: 20 loop : -3.77 (0.25), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 469 HIS 0.013 0.003 HIS B 451 PHE 0.040 0.004 PHE B 468 TYR 0.042 0.004 TYR B 524 ARG 0.016 0.001 ARG B 669 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 202 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 PHE cc_start: 0.9467 (m-10) cc_final: 0.9238 (m-10) REVERT: B 246 LEU cc_start: 0.9680 (tp) cc_final: 0.9375 (mt) REVERT: B 449 TRP cc_start: 0.8575 (m100) cc_final: 0.8317 (m100) REVERT: B 468 PHE cc_start: 0.9160 (p90) cc_final: 0.8846 (p90) REVERT: B 471 SER cc_start: 0.9851 (OUTLIER) cc_final: 0.9239 (p) REVERT: B 490 LEU cc_start: 0.9862 (OUTLIER) cc_final: 0.9430 (mm) REVERT: B 494 PHE cc_start: 0.9472 (m-10) cc_final: 0.9193 (m-80) REVERT: B 502 MET cc_start: 0.9668 (ptt) cc_final: 0.9412 (tmm) REVERT: B 532 LEU cc_start: 0.9596 (tt) cc_final: 0.9237 (mp) REVERT: A 178 PHE cc_start: 0.9448 (m-10) cc_final: 0.9215 (m-10) REVERT: A 449 TRP cc_start: 0.8640 (m100) cc_final: 0.8386 (m100) REVERT: A 468 PHE cc_start: 0.9098 (p90) cc_final: 0.8787 (p90) REVERT: A 471 SER cc_start: 0.9849 (OUTLIER) cc_final: 0.9258 (p) REVERT: A 490 LEU cc_start: 0.9862 (OUTLIER) cc_final: 0.9461 (mm) REVERT: A 494 PHE cc_start: 0.9502 (m-10) cc_final: 0.9226 (m-80) REVERT: A 502 MET cc_start: 0.9603 (ptt) cc_final: 0.9327 (tmm) REVERT: A 532 LEU cc_start: 0.9579 (tt) cc_final: 0.9172 (mp) REVERT: A 663 ARG cc_start: 0.8891 (mtm180) cc_final: 0.8587 (tpm170) outliers start: 20 outliers final: 4 residues processed: 209 average time/residue: 0.1773 time to fit residues: 54.3125 Evaluate side-chains 136 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 47 optimal weight: 0.3980 chunk 92 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 HIS B 379 HIS B 451 HIS B 662 GLN B 838 HIS A 369 HIS A 379 HIS A 451 HIS ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9504 Z= 0.232 Angle : 0.822 13.293 12914 Z= 0.429 Chirality : 0.045 0.174 1526 Planarity : 0.007 0.068 1580 Dihedral : 7.198 51.508 1262 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.65 (0.22), residues: 1182 helix: -0.82 (0.18), residues: 776 sheet: -1.34 (1.08), residues: 20 loop : -3.69 (0.25), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 469 HIS 0.006 0.001 HIS B 451 PHE 0.048 0.003 PHE B 461 TYR 0.025 0.002 TYR B 146 ARG 0.011 0.001 ARG A 669 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 LEU cc_start: 0.9817 (mt) cc_final: 0.9576 (tp) REVERT: B 178 PHE cc_start: 0.9426 (m-10) cc_final: 0.9160 (m-80) REVERT: B 250 MET cc_start: 0.9416 (tpt) cc_final: 0.9131 (ppp) REVERT: B 339 MET cc_start: 0.9360 (pmm) cc_final: 0.9045 (pmm) REVERT: B 490 LEU cc_start: 0.9733 (pp) cc_final: 0.9505 (pp) REVERT: B 494 PHE cc_start: 0.9432 (m-10) cc_final: 0.9161 (m-80) REVERT: B 559 MET cc_start: 0.9717 (ptm) cc_final: 0.8944 (ptp) REVERT: B 653 GLU cc_start: 0.9475 (mt-10) cc_final: 0.9190 (mm-30) REVERT: A 171 LEU cc_start: 0.9813 (mt) cc_final: 0.9537 (tp) REVERT: A 178 PHE cc_start: 0.9387 (m-10) cc_final: 0.9124 (m-80) REVERT: A 250 MET cc_start: 0.9470 (tpt) cc_final: 0.9157 (ppp) REVERT: A 339 MET cc_start: 0.9371 (pmm) cc_final: 0.8979 (pmm) REVERT: A 494 PHE cc_start: 0.9437 (m-10) cc_final: 0.9201 (m-80) REVERT: A 653 GLU cc_start: 0.9491 (mt-10) cc_final: 0.9185 (mm-30) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1765 time to fit residues: 40.3452 Evaluate side-chains 116 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 115 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 379 HIS ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9504 Z= 0.217 Angle : 0.787 12.396 12914 Z= 0.403 Chirality : 0.044 0.175 1526 Planarity : 0.006 0.050 1580 Dihedral : 6.675 49.558 1262 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 0.40 % Allowed : 5.57 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.94 (0.23), residues: 1182 helix: -0.20 (0.18), residues: 782 sheet: -1.23 (1.02), residues: 20 loop : -3.63 (0.25), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 469 HIS 0.004 0.001 HIS B 835 PHE 0.036 0.002 PHE B 306 TYR 0.028 0.002 TYR B 146 ARG 0.004 0.001 ARG B 300 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 162 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 LEU cc_start: 0.9816 (mt) cc_final: 0.9520 (tp) REVERT: B 178 PHE cc_start: 0.9380 (m-10) cc_final: 0.9121 (m-80) REVERT: B 232 GLU cc_start: 0.9589 (OUTLIER) cc_final: 0.9257 (pt0) REVERT: B 250 MET cc_start: 0.9460 (tpt) cc_final: 0.9153 (ppp) REVERT: B 339 MET cc_start: 0.9342 (pmm) cc_final: 0.8968 (pmm) REVERT: B 468 PHE cc_start: 0.9113 (p90) cc_final: 0.8730 (p90) REVERT: B 490 LEU cc_start: 0.9730 (pp) cc_final: 0.9482 (pp) REVERT: B 494 PHE cc_start: 0.9370 (m-10) cc_final: 0.9093 (m-80) REVERT: B 653 GLU cc_start: 0.9483 (mt-10) cc_final: 0.9278 (mm-30) REVERT: A 124 LEU cc_start: 0.9751 (tt) cc_final: 0.9422 (tt) REVERT: A 128 MET cc_start: 0.9696 (mmp) cc_final: 0.9461 (mmm) REVERT: A 171 LEU cc_start: 0.9813 (mt) cc_final: 0.9506 (tp) REVERT: A 178 PHE cc_start: 0.9381 (m-10) cc_final: 0.9130 (m-80) REVERT: A 232 GLU cc_start: 0.9600 (OUTLIER) cc_final: 0.9260 (pt0) REVERT: A 250 MET cc_start: 0.9486 (tpt) cc_final: 0.9175 (ppp) REVERT: A 311 PHE cc_start: 0.9100 (m-80) cc_final: 0.8872 (m-80) REVERT: A 339 MET cc_start: 0.9333 (pmm) cc_final: 0.8940 (pmm) REVERT: A 468 PHE cc_start: 0.9099 (p90) cc_final: 0.8800 (p90) REVERT: A 494 PHE cc_start: 0.9417 (m-10) cc_final: 0.9062 (m-80) REVERT: A 532 LEU cc_start: 0.9432 (tp) cc_final: 0.9212 (tp) REVERT: A 559 MET cc_start: 0.9668 (ptm) cc_final: 0.9376 (ptm) REVERT: A 653 GLU cc_start: 0.9488 (mt-10) cc_final: 0.9188 (mm-30) outliers start: 4 outliers final: 0 residues processed: 164 average time/residue: 0.1943 time to fit residues: 47.5859 Evaluate side-chains 123 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 chunk 72 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9504 Z= 0.212 Angle : 0.773 11.840 12914 Z= 0.392 Chirality : 0.044 0.148 1526 Planarity : 0.006 0.050 1580 Dihedral : 6.348 48.200 1262 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.47 (0.24), residues: 1182 helix: 0.13 (0.19), residues: 782 sheet: -1.08 (1.01), residues: 20 loop : -3.35 (0.27), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 469 HIS 0.005 0.001 HIS B 664 PHE 0.038 0.002 PHE B 463 TYR 0.025 0.002 TYR B 146 ARG 0.003 0.000 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 LEU cc_start: 0.9816 (mt) cc_final: 0.9521 (tp) REVERT: B 178 PHE cc_start: 0.9349 (m-10) cc_final: 0.9111 (m-80) REVERT: B 250 MET cc_start: 0.9493 (tpt) cc_final: 0.9163 (ppp) REVERT: B 339 MET cc_start: 0.9379 (pmm) cc_final: 0.9115 (pmm) REVERT: B 466 MET cc_start: 0.9418 (tpt) cc_final: 0.9162 (tpp) REVERT: B 490 LEU cc_start: 0.9732 (pp) cc_final: 0.9445 (pp) REVERT: B 494 PHE cc_start: 0.9278 (m-10) cc_final: 0.8991 (m-80) REVERT: B 559 MET cc_start: 0.9696 (ptm) cc_final: 0.8970 (ppp) REVERT: B 560 MET cc_start: 0.9844 (mpp) cc_final: 0.9361 (mpp) REVERT: B 653 GLU cc_start: 0.9475 (mt-10) cc_final: 0.9204 (mm-30) REVERT: B 663 ARG cc_start: 0.7859 (tpm170) cc_final: 0.7643 (tpm170) REVERT: A 171 LEU cc_start: 0.9812 (mt) cc_final: 0.9504 (tp) REVERT: A 178 PHE cc_start: 0.9369 (m-10) cc_final: 0.9122 (m-80) REVERT: A 250 MET cc_start: 0.9557 (tpt) cc_final: 0.9230 (ppp) REVERT: A 311 PHE cc_start: 0.9076 (m-80) cc_final: 0.8781 (m-80) REVERT: A 339 MET cc_start: 0.9357 (pmm) cc_final: 0.9106 (pmm) REVERT: A 466 MET cc_start: 0.9429 (tpt) cc_final: 0.9184 (tpp) REVERT: A 494 PHE cc_start: 0.9328 (m-10) cc_final: 0.8966 (m-80) REVERT: A 532 LEU cc_start: 0.9364 (tp) cc_final: 0.9119 (tp) REVERT: A 559 MET cc_start: 0.9665 (ptm) cc_final: 0.9366 (ptm) REVERT: A 609 MET cc_start: 0.8965 (pmm) cc_final: 0.8759 (pmm) REVERT: A 653 GLU cc_start: 0.9486 (mt-10) cc_final: 0.9181 (mm-30) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1718 time to fit residues: 40.6628 Evaluate side-chains 120 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.0270 chunk 64 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 84 optimal weight: 0.1980 chunk 47 optimal weight: 0.2980 chunk 97 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.5040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 HIS B 658 GLN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9504 Z= 0.188 Angle : 0.753 11.305 12914 Z= 0.379 Chirality : 0.045 0.158 1526 Planarity : 0.005 0.049 1580 Dihedral : 6.065 46.698 1262 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.11 (0.24), residues: 1182 helix: 0.46 (0.19), residues: 756 sheet: -0.87 (0.99), residues: 20 loop : -3.11 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 449 HIS 0.004 0.001 HIS B 389 PHE 0.031 0.002 PHE B 484 TYR 0.023 0.001 TYR B 146 ARG 0.003 0.000 ARG B 496 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 LEU cc_start: 0.9806 (mt) cc_final: 0.9488 (tp) REVERT: B 178 PHE cc_start: 0.9325 (m-10) cc_final: 0.9023 (m-80) REVERT: B 209 MET cc_start: 0.9577 (pmm) cc_final: 0.9178 (tmm) REVERT: B 250 MET cc_start: 0.9506 (tpt) cc_final: 0.9156 (ppp) REVERT: B 339 MET cc_start: 0.9328 (pmm) cc_final: 0.8981 (pmm) REVERT: B 468 PHE cc_start: 0.9103 (p90) cc_final: 0.8621 (p90) REVERT: B 485 MET cc_start: 0.9622 (mtm) cc_final: 0.9411 (mtm) REVERT: B 490 LEU cc_start: 0.9740 (pp) cc_final: 0.9448 (pp) REVERT: B 494 PHE cc_start: 0.9274 (m-10) cc_final: 0.8997 (m-80) REVERT: B 547 PHE cc_start: 0.9524 (p90) cc_final: 0.9189 (p90) REVERT: B 609 MET cc_start: 0.8853 (pmm) cc_final: 0.8624 (pmm) REVERT: B 663 ARG cc_start: 0.7919 (tpm170) cc_final: 0.7669 (tpm170) REVERT: A 128 MET cc_start: 0.9740 (mmp) cc_final: 0.9497 (ttm) REVERT: A 171 LEU cc_start: 0.9798 (mt) cc_final: 0.9457 (tp) REVERT: A 178 PHE cc_start: 0.9304 (m-10) cc_final: 0.8975 (m-80) REVERT: A 250 MET cc_start: 0.9552 (tpt) cc_final: 0.9239 (ppp) REVERT: A 311 PHE cc_start: 0.9096 (m-80) cc_final: 0.8758 (m-80) REVERT: A 339 MET cc_start: 0.9338 (pmm) cc_final: 0.8936 (pmm) REVERT: A 345 LEU cc_start: 0.9800 (pt) cc_final: 0.9590 (mt) REVERT: A 461 PHE cc_start: 0.9531 (m-80) cc_final: 0.9312 (m-10) REVERT: A 464 PHE cc_start: 0.9033 (p90) cc_final: 0.8774 (p90) REVERT: A 468 PHE cc_start: 0.8976 (p90) cc_final: 0.8576 (p90) REVERT: A 490 LEU cc_start: 0.9799 (pp) cc_final: 0.9584 (pp) REVERT: A 494 PHE cc_start: 0.9306 (m-10) cc_final: 0.9009 (m-80) REVERT: A 532 LEU cc_start: 0.9316 (tp) cc_final: 0.9071 (tp) REVERT: A 559 MET cc_start: 0.9620 (ptm) cc_final: 0.9325 (ptm) REVERT: A 609 MET cc_start: 0.8950 (pmm) cc_final: 0.8676 (pmm) REVERT: A 653 GLU cc_start: 0.9438 (mt-10) cc_final: 0.9161 (mm-30) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1682 time to fit residues: 42.4831 Evaluate side-chains 125 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 66 optimal weight: 0.0870 chunk 28 optimal weight: 2.9990 chunk 114 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9504 Z= 0.244 Angle : 0.794 14.216 12914 Z= 0.399 Chirality : 0.045 0.189 1526 Planarity : 0.005 0.047 1580 Dihedral : 6.140 44.801 1262 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.13 (0.24), residues: 1182 helix: 0.35 (0.18), residues: 782 sheet: -0.77 (1.01), residues: 20 loop : -3.14 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 433 HIS 0.003 0.001 HIS B 835 PHE 0.024 0.002 PHE B 547 TYR 0.022 0.002 TYR A 146 ARG 0.004 0.000 ARG B 654 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 LEU cc_start: 0.9811 (mt) cc_final: 0.9478 (tt) REVERT: B 178 PHE cc_start: 0.9407 (m-10) cc_final: 0.9107 (m-80) REVERT: B 209 MET cc_start: 0.9573 (pmm) cc_final: 0.9182 (tmm) REVERT: B 250 MET cc_start: 0.9561 (tpt) cc_final: 0.9193 (ppp) REVERT: B 339 MET cc_start: 0.9342 (pmm) cc_final: 0.9008 (pmm) REVERT: B 468 PHE cc_start: 0.9140 (p90) cc_final: 0.8911 (p90) REVERT: B 490 LEU cc_start: 0.9824 (pp) cc_final: 0.9529 (pp) REVERT: B 494 PHE cc_start: 0.9229 (m-10) cc_final: 0.8939 (m-80) REVERT: B 532 LEU cc_start: 0.9337 (tp) cc_final: 0.9060 (tp) REVERT: B 663 ARG cc_start: 0.7893 (tpm170) cc_final: 0.7677 (tpm170) REVERT: A 178 PHE cc_start: 0.9382 (m-10) cc_final: 0.9092 (m-80) REVERT: A 250 MET cc_start: 0.9577 (tpt) cc_final: 0.9223 (ppp) REVERT: A 311 PHE cc_start: 0.9125 (m-80) cc_final: 0.8785 (m-80) REVERT: A 325 ASP cc_start: 0.8396 (m-30) cc_final: 0.8071 (p0) REVERT: A 339 MET cc_start: 0.9321 (pmm) cc_final: 0.8922 (pmm) REVERT: A 490 LEU cc_start: 0.9803 (pp) cc_final: 0.9595 (pp) REVERT: A 494 PHE cc_start: 0.9227 (m-10) cc_final: 0.8943 (m-80) REVERT: A 527 ILE cc_start: 0.9268 (pt) cc_final: 0.9036 (pt) REVERT: A 532 LEU cc_start: 0.9170 (tp) cc_final: 0.8917 (tp) REVERT: A 653 GLU cc_start: 0.9475 (mt-10) cc_final: 0.9173 (mm-30) REVERT: A 663 ARG cc_start: 0.7891 (tpm170) cc_final: 0.7688 (tpm170) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1647 time to fit residues: 38.1263 Evaluate side-chains 114 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.1980 chunk 12 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 113 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9504 Z= 0.196 Angle : 0.776 10.514 12914 Z= 0.387 Chirality : 0.045 0.181 1526 Planarity : 0.005 0.049 1580 Dihedral : 5.922 44.961 1262 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.75 (0.24), residues: 1182 helix: 0.76 (0.19), residues: 746 sheet: -0.67 (1.00), residues: 20 loop : -2.92 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 469 HIS 0.007 0.001 HIS B 847 PHE 0.026 0.002 PHE A 547 TYR 0.021 0.001 TYR A 146 ARG 0.003 0.000 ARG A 669 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 LEU cc_start: 0.9784 (mt) cc_final: 0.9440 (tp) REVERT: B 178 PHE cc_start: 0.9357 (m-10) cc_final: 0.9103 (m-80) REVERT: B 209 MET cc_start: 0.9575 (pmm) cc_final: 0.9205 (tmm) REVERT: B 250 MET cc_start: 0.9568 (tpt) cc_final: 0.9171 (ppp) REVERT: B 490 LEU cc_start: 0.9806 (pp) cc_final: 0.9595 (pp) REVERT: B 494 PHE cc_start: 0.9277 (m-10) cc_final: 0.8997 (m-80) REVERT: B 547 PHE cc_start: 0.9524 (p90) cc_final: 0.9196 (p90) REVERT: B 609 MET cc_start: 0.8945 (pmm) cc_final: 0.8722 (pmm) REVERT: B 663 ARG cc_start: 0.7721 (tpm170) cc_final: 0.7489 (tpm170) REVERT: A 124 LEU cc_start: 0.9677 (tt) cc_final: 0.9295 (tt) REVERT: A 171 LEU cc_start: 0.9782 (mt) cc_final: 0.9471 (tt) REVERT: A 178 PHE cc_start: 0.9361 (m-10) cc_final: 0.9124 (m-80) REVERT: A 250 MET cc_start: 0.9604 (tpt) cc_final: 0.9269 (ppp) REVERT: A 311 PHE cc_start: 0.9124 (m-80) cc_final: 0.8774 (m-80) REVERT: A 325 ASP cc_start: 0.8169 (m-30) cc_final: 0.7957 (p0) REVERT: A 468 PHE cc_start: 0.8997 (p90) cc_final: 0.8642 (p90) REVERT: A 490 LEU cc_start: 0.9815 (pp) cc_final: 0.9591 (pp) REVERT: A 494 PHE cc_start: 0.9196 (m-10) cc_final: 0.8920 (m-80) REVERT: A 532 LEU cc_start: 0.9173 (tp) cc_final: 0.8934 (tp) REVERT: A 547 PHE cc_start: 0.9545 (p90) cc_final: 0.9201 (p90) REVERT: A 559 MET cc_start: 0.9704 (ptm) cc_final: 0.9496 (ptm) REVERT: A 653 GLU cc_start: 0.9450 (mt-10) cc_final: 0.9188 (mm-30) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1789 time to fit residues: 47.0285 Evaluate side-chains 126 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 72 optimal weight: 0.0970 chunk 77 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9504 Z= 0.199 Angle : 0.826 13.429 12914 Z= 0.412 Chirality : 0.046 0.278 1526 Planarity : 0.005 0.049 1580 Dihedral : 5.802 43.532 1262 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 1182 helix: 0.67 (0.19), residues: 758 sheet: -0.35 (0.97), residues: 20 loop : -2.91 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 469 HIS 0.005 0.001 HIS B 847 PHE 0.049 0.002 PHE B 464 TYR 0.019 0.001 TYR A 146 ARG 0.003 0.000 ARG A 663 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 209 MET cc_start: 0.9565 (pmm) cc_final: 0.9194 (tmm) REVERT: B 250 MET cc_start: 0.9574 (tpt) cc_final: 0.9190 (ppp) REVERT: B 345 LEU cc_start: 0.9790 (pt) cc_final: 0.9590 (mt) REVERT: B 468 PHE cc_start: 0.9134 (p90) cc_final: 0.8830 (p90) REVERT: B 490 LEU cc_start: 0.9832 (pp) cc_final: 0.9618 (pp) REVERT: B 494 PHE cc_start: 0.9299 (m-10) cc_final: 0.9062 (m-80) REVERT: B 527 ILE cc_start: 0.9188 (pt) cc_final: 0.8984 (pt) REVERT: B 547 PHE cc_start: 0.9508 (p90) cc_final: 0.9092 (p90) REVERT: B 559 MET cc_start: 0.9690 (ptm) cc_final: 0.9450 (ptm) REVERT: B 609 MET cc_start: 0.8848 (pmm) cc_final: 0.8587 (pmm) REVERT: B 663 ARG cc_start: 0.7593 (tpm170) cc_final: 0.7344 (tpm170) REVERT: A 250 MET cc_start: 0.9574 (tpt) cc_final: 0.9247 (ppp) REVERT: A 311 PHE cc_start: 0.9145 (m-80) cc_final: 0.8791 (m-80) REVERT: A 461 PHE cc_start: 0.9542 (m-80) cc_final: 0.9285 (m-80) REVERT: A 464 PHE cc_start: 0.9020 (p90) cc_final: 0.8686 (p90) REVERT: A 468 PHE cc_start: 0.9048 (p90) cc_final: 0.8661 (p90) REVERT: A 490 LEU cc_start: 0.9775 (pp) cc_final: 0.9556 (pp) REVERT: A 494 PHE cc_start: 0.9125 (m-10) cc_final: 0.8801 (m-80) REVERT: A 504 MET cc_start: 0.9601 (tmm) cc_final: 0.9361 (ppp) REVERT: A 547 PHE cc_start: 0.9509 (p90) cc_final: 0.9282 (p90) REVERT: A 653 GLU cc_start: 0.9442 (mt-10) cc_final: 0.9193 (mm-30) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1690 time to fit residues: 43.4761 Evaluate side-chains 125 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- 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: 65.6344 > 50: distance: 58 - 59: 5.341 distance: 59 - 60: 6.761 distance: 59 - 62: 22.367 distance: 60 - 61: 18.093 distance: 60 - 64: 17.943 distance: 62 - 63: 13.276 distance: 64 - 65: 4.853 distance: 65 - 66: 13.522 distance: 65 - 68: 18.721 distance: 66 - 67: 36.752 distance: 66 - 72: 29.116 distance: 68 - 69: 15.149 distance: 69 - 70: 16.336 distance: 69 - 71: 31.228 distance: 72 - 73: 16.335 distance: 73 - 74: 8.443 distance: 74 - 76: 8.715 distance: 75 - 91: 18.699 distance: 76 - 77: 19.776 distance: 77 - 78: 20.465 distance: 77 - 80: 25.505 distance: 78 - 79: 8.844 distance: 78 - 85: 4.070 distance: 79 - 96: 42.699 distance: 80 - 81: 8.492 distance: 81 - 82: 16.296 distance: 82 - 83: 28.658 distance: 82 - 84: 32.525 distance: 85 - 86: 5.611 distance: 86 - 87: 14.926 distance: 86 - 89: 10.426 distance: 87 - 88: 17.257 distance: 87 - 91: 16.284 distance: 88 - 103: 35.842 distance: 89 - 90: 23.731 distance: 92 - 93: 21.565 distance: 92 - 95: 16.157 distance: 93 - 94: 9.020 distance: 93 - 96: 24.960 distance: 96 - 97: 13.963 distance: 97 - 98: 13.228 distance: 97 - 100: 13.708 distance: 98 - 99: 10.563 distance: 98 - 103: 18.658 distance: 100 - 101: 11.919 distance: 100 - 102: 21.907 distance: 103 - 104: 14.966 distance: 104 - 105: 3.213 distance: 104 - 107: 6.586 distance: 105 - 106: 4.941 distance: 105 - 117: 11.362 distance: 107 - 108: 3.134 distance: 108 - 110: 6.513 distance: 109 - 111: 8.417 distance: 110 - 112: 5.637 distance: 110 - 113: 4.627 distance: 111 - 112: 5.812 distance: 112 - 114: 8.026 distance: 113 - 115: 7.799 distance: 114 - 116: 3.875 distance: 115 - 116: 4.824 distance: 117 - 118: 11.179 distance: 118 - 119: 19.777 distance: 118 - 121: 12.665 distance: 119 - 120: 29.398 distance: 119 - 125: 5.213 distance: 121 - 122: 20.116 distance: 121 - 123: 13.229 distance: 122 - 124: 13.436 distance: 125 - 126: 8.557 distance: 126 - 127: 12.287 distance: 126 - 129: 9.754 distance: 127 - 128: 5.403 distance: 127 - 135: 17.054 distance: 129 - 130: 13.004 distance: 130 - 131: 13.790 distance: 130 - 132: 26.160 distance: 131 - 133: 19.254 distance: 132 - 134: 14.462 distance: 133 - 134: 17.041