Starting phenix.real_space_refine on Thu Mar 14 16:37:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvu_4657/03_2024/6qvu_4657.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvu_4657/03_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_4657/03_2024/6qvu_4657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvu_4657/03_2024/6qvu_4657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvu_4657/03_2024/6qvu_4657.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvu_4657/03_2024/6qvu_4657.pdb" } 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-5265/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: 5.27, per 1000 atoms: 0.57 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: 3.23 Conformation dependent library (CDL) restraints added in 1.6 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: 0.85 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: 2.55 Time building geometry restraints manager: 3.55 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 2.440 nonbonded pdb=" O ILE B 401 " pdb=" OG1 THR B 405 " model vdw 2.192 2.440 nonbonded pdb=" O ILE B 472 " pdb=" OG1 THR B 476 " model vdw 2.255 2.440 nonbonded pdb=" O ILE A 472 " pdb=" OG1 THR A 476 " model vdw 2.256 2.440 nonbonded pdb=" OH TYR B 302 " pdb=" O GLU A 291 " model vdw 2.262 2.440 ... (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 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: 0.010 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.330 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 26.770 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.520 ------------------------------------------------------------------------------- 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 : 1.076 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: 0.1756 time to fit residues: 53.8177 Evaluate side-chains 136 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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: 1.9990 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 92 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 107 optimal weight: 0.0870 overall best weight: 2.6166 ------------------------------------------------------------------------------- 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 436 HIS B 451 HIS ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 HIS A 152 GLN A 369 HIS A 379 HIS A 436 HIS A 451 HIS ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9504 Z= 0.242 Angle : 0.815 14.021 12914 Z= 0.426 Chirality : 0.045 0.175 1526 Planarity : 0.007 0.053 1580 Dihedral : 7.138 51.239 1262 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 22.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % 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: -2.63 (0.22), residues: 1182 helix: -0.80 (0.18), residues: 778 sheet: -1.74 (1.06), residues: 20 loop : -3.69 (0.25), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 469 HIS 0.006 0.001 HIS B 451 PHE 0.046 0.003 PHE B 461 TYR 0.025 0.002 TYR B 146 ARG 0.010 0.001 ARG B 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 152 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.044 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: 0.9821 (mt) cc_final: 0.9577 (tp) REVERT: B 178 PHE cc_start: 0.9414 (m-10) cc_final: 0.9156 (m-80) REVERT: B 250 MET cc_start: 0.9441 (tpt) cc_final: 0.9136 (ppp) REVERT: B 273 VAL cc_start: 0.9425 (t) cc_final: 0.9088 (p) REVERT: B 339 MET cc_start: 0.9290 (pmm) cc_final: 0.8967 (pmm) REVERT: B 490 LEU cc_start: 0.9739 (pp) cc_final: 0.9500 (pp) REVERT: B 494 PHE cc_start: 0.9436 (m-10) cc_final: 0.9176 (m-80) REVERT: B 609 MET cc_start: 0.8844 (pmm) cc_final: 0.8582 (pmm) REVERT: B 653 GLU cc_start: 0.9482 (mt-10) cc_final: 0.9210 (mm-30) REVERT: A 171 LEU cc_start: 0.9810 (mt) cc_final: 0.9518 (tp) REVERT: A 178 PHE cc_start: 0.9388 (m-10) cc_final: 0.9125 (m-80) REVERT: A 250 MET cc_start: 0.9476 (tpt) cc_final: 0.9144 (ppp) REVERT: A 339 MET cc_start: 0.9310 (pmm) cc_final: 0.8944 (pmm) REVERT: A 494 PHE cc_start: 0.9431 (m-10) cc_final: 0.9210 (m-80) REVERT: A 653 GLU cc_start: 0.9475 (mt-10) cc_final: 0.9191 (mm-30) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1756 time to fit residues: 39.4424 Evaluate side-chains 117 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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: 5.9990 chunk 89 optimal weight: 0.0060 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 379 HIS ** B 662 GLN ** 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: 0.7654 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9504 Z= 0.196 Angle : 0.766 11.440 12914 Z= 0.392 Chirality : 0.044 0.190 1526 Planarity : 0.006 0.052 1580 Dihedral : 6.656 49.537 1262 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.20 % Allowed : 4.97 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -1.90 (0.23), residues: 1182 helix: -0.15 (0.18), residues: 782 sheet: -1.52 (0.99), residues: 20 loop : -3.62 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 469 HIS 0.005 0.001 HIS A 379 PHE 0.039 0.002 PHE B 306 TYR 0.027 0.002 TYR B 146 ARG 0.003 0.000 ARG A 663 *********************** 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 165 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 163 time to evaluate : 0.946 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: B 171 LEU cc_start: 0.9807 (mt) cc_final: 0.9512 (tp) REVERT: B 178 PHE cc_start: 0.9336 (m-10) cc_final: 0.9093 (m-80) REVERT: B 250 MET cc_start: 0.9444 (tpt) cc_final: 0.9143 (ppp) REVERT: B 339 MET cc_start: 0.9250 (pmm) cc_final: 0.8874 (pmm) REVERT: B 468 PHE cc_start: 0.9067 (p90) cc_final: 0.8694 (p90) REVERT: B 490 LEU cc_start: 0.9738 (pp) cc_final: 0.9478 (pp) REVERT: B 494 PHE cc_start: 0.9368 (m-10) cc_final: 0.9128 (m-80) REVERT: B 559 MET cc_start: 0.9676 (ptm) cc_final: 0.8938 (ppp) REVERT: B 560 MET cc_start: 0.9855 (mpp) cc_final: 0.9383 (mpp) REVERT: B 609 MET cc_start: 0.8794 (pmm) cc_final: 0.8578 (pmm) REVERT: B 653 GLU cc_start: 0.9450 (mt-10) cc_final: 0.9247 (mm-30) REVERT: A 124 LEU cc_start: 0.9745 (tt) cc_final: 0.9422 (tt) REVERT: A 128 MET cc_start: 0.9697 (mmp) cc_final: 0.9469 (mmm) REVERT: A 171 LEU cc_start: 0.9807 (mt) cc_final: 0.9500 (tp) REVERT: A 178 PHE cc_start: 0.9340 (m-10) cc_final: 0.9098 (m-80) REVERT: A 250 MET cc_start: 0.9482 (tpt) cc_final: 0.9159 (ppp) REVERT: A 311 PHE cc_start: 0.9089 (m-80) cc_final: 0.8861 (m-80) REVERT: A 339 MET cc_start: 0.9289 (pmm) cc_final: 0.8935 (pmm) REVERT: A 468 PHE cc_start: 0.9102 (p90) cc_final: 0.8825 (p90) REVERT: A 490 LEU cc_start: 0.9817 (pp) cc_final: 0.9597 (pp) REVERT: A 494 PHE cc_start: 0.9402 (m-10) cc_final: 0.9141 (m-80) REVERT: A 559 MET cc_start: 0.9682 (ptm) cc_final: 0.9394 (ptm) REVERT: A 609 MET cc_start: 0.8959 (pmm) cc_final: 0.8741 (pmm) REVERT: A 653 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9160 (mm-30) outliers start: 2 outliers final: 0 residues processed: 165 average time/residue: 0.1627 time to fit residues: 40.1570 Evaluate side-chains 116 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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: 10.0000 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 chunk 72 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9504 Z= 0.207 Angle : 0.754 11.168 12914 Z= 0.381 Chirality : 0.044 0.146 1526 Planarity : 0.005 0.052 1580 Dihedral : 6.275 48.061 1262 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % 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: -1.50 (0.24), residues: 1182 helix: 0.16 (0.19), residues: 780 sheet: -1.38 (0.96), residues: 20 loop : -3.47 (0.27), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 469 HIS 0.002 0.001 HIS B 835 PHE 0.029 0.002 PHE B 461 TYR 0.025 0.002 TYR B 146 ARG 0.004 0.000 ARG B 300 *********************** 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 160 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.998 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: B 171 LEU cc_start: 0.9806 (mt) cc_final: 0.9497 (tp) REVERT: B 178 PHE cc_start: 0.9319 (m-10) cc_final: 0.9082 (m-80) REVERT: B 250 MET cc_start: 0.9488 (tpt) cc_final: 0.9145 (ppp) REVERT: B 339 MET cc_start: 0.9267 (pmm) cc_final: 0.8987 (pmm) REVERT: B 468 PHE cc_start: 0.9079 (p90) cc_final: 0.8877 (p90) REVERT: B 490 LEU cc_start: 0.9758 (pp) cc_final: 0.9499 (pp) REVERT: B 494 PHE cc_start: 0.9298 (m-10) cc_final: 0.9022 (m-80) REVERT: B 559 MET cc_start: 0.9670 (ptm) cc_final: 0.8971 (ppp) REVERT: B 560 MET cc_start: 0.9843 (mpp) cc_final: 0.9338 (mpp) REVERT: B 663 ARG cc_start: 0.7980 (tpm170) cc_final: 0.7750 (tpm170) REVERT: A 171 LEU cc_start: 0.9806 (mt) cc_final: 0.9501 (tp) REVERT: A 178 PHE cc_start: 0.9330 (m-10) cc_final: 0.9073 (m-80) REVERT: A 250 MET cc_start: 0.9553 (tpt) cc_final: 0.9215 (ppp) REVERT: A 311 PHE cc_start: 0.9074 (m-80) cc_final: 0.8781 (m-80) REVERT: A 339 MET cc_start: 0.9321 (pmm) cc_final: 0.9072 (pmm) REVERT: A 345 LEU cc_start: 0.9785 (pt) cc_final: 0.9535 (mt) REVERT: A 468 PHE cc_start: 0.9057 (p90) cc_final: 0.8758 (p90) REVERT: A 494 PHE cc_start: 0.9335 (m-10) cc_final: 0.9010 (m-80) REVERT: A 559 MET cc_start: 0.9649 (ptm) cc_final: 0.9353 (ptm) REVERT: A 653 GLU cc_start: 0.9425 (mt-10) cc_final: 0.9179 (mm-30) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1714 time to fit residues: 40.6773 Evaluate side-chains 114 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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: 7.9990 chunk 64 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 0.0980 chunk 97 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 chunk 28 optimal weight: 0.0670 overall best weight: 1.3120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9504 Z= 0.202 Angle : 0.746 12.367 12914 Z= 0.379 Chirality : 0.044 0.155 1526 Planarity : 0.005 0.051 1580 Dihedral : 6.059 46.644 1262 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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: -1.27 (0.24), residues: 1182 helix: 0.31 (0.18), residues: 784 sheet: -1.16 (0.98), residues: 20 loop : -3.33 (0.27), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 449 HIS 0.003 0.001 HIS B 389 PHE 0.039 0.002 PHE A 463 TYR 0.024 0.002 TYR B 146 ARG 0.004 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 159 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.973 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: 0.9803 (mt) cc_final: 0.9466 (tp) REVERT: B 178 PHE cc_start: 0.9334 (m-10) cc_final: 0.9034 (m-80) REVERT: B 209 MET cc_start: 0.9584 (pmm) cc_final: 0.9210 (tmm) REVERT: B 250 MET cc_start: 0.9547 (tpt) cc_final: 0.9182 (ppp) REVERT: B 339 MET cc_start: 0.9239 (pmm) cc_final: 0.8850 (pmm) REVERT: B 461 PHE cc_start: 0.9521 (m-80) cc_final: 0.9290 (m-80) REVERT: B 466 MET cc_start: 0.9376 (tpt) cc_final: 0.8941 (tmm) REVERT: B 468 PHE cc_start: 0.9039 (p90) cc_final: 0.8824 (p90) REVERT: B 490 LEU cc_start: 0.9757 (pp) cc_final: 0.9481 (pp) REVERT: B 494 PHE cc_start: 0.9268 (m-10) cc_final: 0.9034 (m-80) REVERT: B 609 MET cc_start: 0.8905 (pmm) cc_final: 0.8673 (pmm) REVERT: A 124 LEU cc_start: 0.9648 (tt) cc_final: 0.9275 (tt) REVERT: A 171 LEU cc_start: 0.9798 (mt) cc_final: 0.9451 (tp) REVERT: A 250 MET cc_start: 0.9550 (tpt) cc_final: 0.9208 (ppp) REVERT: A 311 PHE cc_start: 0.9085 (m-80) cc_final: 0.8760 (m-80) REVERT: A 339 MET cc_start: 0.9298 (pmm) cc_final: 0.8912 (pmm) REVERT: A 345 LEU cc_start: 0.9794 (pt) cc_final: 0.9571 (mt) REVERT: A 461 PHE cc_start: 0.9520 (m-80) cc_final: 0.9267 (m-80) REVERT: A 466 MET cc_start: 0.9438 (tpt) cc_final: 0.9220 (tmm) REVERT: A 468 PHE cc_start: 0.9018 (p90) cc_final: 0.8677 (p90) REVERT: A 494 PHE cc_start: 0.9317 (m-10) cc_final: 0.9060 (m-80) REVERT: A 527 ILE cc_start: 0.9222 (pt) cc_final: 0.8968 (pt) REVERT: A 532 LEU cc_start: 0.9188 (tp) cc_final: 0.8890 (tp) REVERT: A 559 MET cc_start: 0.9650 (ptm) cc_final: 0.9436 (ptm) REVERT: A 653 GLU cc_start: 0.9422 (mt-10) cc_final: 0.9159 (mm-30) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1746 time to fit residues: 41.3917 Evaluate side-chains 118 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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: 6.9990 chunk 102 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 66 optimal weight: 0.0470 chunk 28 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 94 optimal weight: 0.3980 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4351 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= 0.204 Angle : 0.794 12.580 12914 Z= 0.393 Chirality : 0.045 0.281 1526 Planarity : 0.005 0.047 1580 Dihedral : 6.043 46.446 1262 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % 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: -0.97 (0.24), residues: 1182 helix: 0.62 (0.19), residues: 768 sheet: -1.03 (0.98), residues: 20 loop : -3.29 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 469 HIS 0.002 0.001 HIS B 835 PHE 0.031 0.002 PHE B 484 TYR 0.021 0.002 TYR B 146 ARG 0.004 0.000 ARG A 496 *********************** 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 161 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 LEU cc_start: 0.9803 (mt) cc_final: 0.9466 (tt) REVERT: B 178 PHE cc_start: 0.9342 (m-10) cc_final: 0.9058 (m-80) REVERT: B 209 MET cc_start: 0.9587 (pmm) cc_final: 0.9174 (tmm) REVERT: B 250 MET cc_start: 0.9551 (tpt) cc_final: 0.9169 (ppp) REVERT: B 339 MET cc_start: 0.9235 (pmm) cc_final: 0.8841 (pmm) REVERT: B 461 PHE cc_start: 0.9578 (m-80) cc_final: 0.9333 (m-80) REVERT: B 466 MET cc_start: 0.9439 (tpt) cc_final: 0.9201 (tmm) REVERT: B 468 PHE cc_start: 0.9063 (p90) cc_final: 0.8792 (p90) REVERT: B 470 MET cc_start: 0.9386 (ppp) cc_final: 0.9112 (ppp) REVERT: B 490 LEU cc_start: 0.9828 (pp) cc_final: 0.9553 (pp) REVERT: B 494 PHE cc_start: 0.9276 (m-10) cc_final: 0.9016 (m-80) REVERT: B 532 LEU cc_start: 0.9256 (tp) cc_final: 0.9021 (tp) REVERT: B 547 PHE cc_start: 0.9487 (p90) cc_final: 0.9139 (p90) REVERT: B 559 MET cc_start: 0.9655 (ptm) cc_final: 0.9380 (ptm) REVERT: A 171 LEU cc_start: 0.9799 (mt) cc_final: 0.9450 (tt) REVERT: A 178 PHE cc_start: 0.9352 (m-10) cc_final: 0.9052 (m-80) REVERT: A 250 MET cc_start: 0.9538 (tpt) cc_final: 0.9193 (ppp) REVERT: A 311 PHE cc_start: 0.9089 (m-80) cc_final: 0.8747 (m-80) REVERT: A 339 MET cc_start: 0.9278 (pmm) cc_final: 0.8897 (pmm) REVERT: A 468 PHE cc_start: 0.8973 (p90) cc_final: 0.8721 (p90) REVERT: A 494 PHE cc_start: 0.9238 (m-10) cc_final: 0.8947 (m-80) REVERT: A 527 ILE cc_start: 0.9227 (pt) cc_final: 0.8972 (pt) REVERT: A 532 LEU cc_start: 0.9225 (tp) cc_final: 0.8918 (tp) REVERT: A 653 GLU cc_start: 0.9428 (mt-10) cc_final: 0.9172 (mm-30) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1688 time to fit residues: 40.5935 Evaluate side-chains 120 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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: 6.9990 chunk 12 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 64 optimal weight: 0.0870 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 52 optimal weight: 20.0000 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9504 Z= 0.200 Angle : 0.787 11.072 12914 Z= 0.388 Chirality : 0.045 0.191 1526 Planarity : 0.005 0.049 1580 Dihedral : 5.878 46.598 1262 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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: -0.82 (0.24), residues: 1182 helix: 0.74 (0.19), residues: 756 sheet: -0.95 (0.96), residues: 20 loop : -3.12 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 469 HIS 0.003 0.001 HIS A 436 PHE 0.034 0.002 PHE A 464 TYR 0.022 0.001 TYR B 146 ARG 0.003 0.000 ARG A 663 *********************** 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 170 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 171 LEU cc_start: 0.9783 (mt) cc_final: 0.9429 (tt) REVERT: B 178 PHE cc_start: 0.9331 (m-10) cc_final: 0.9075 (m-80) REVERT: B 209 MET cc_start: 0.9551 (pmm) cc_final: 0.9126 (tmm) REVERT: B 250 MET cc_start: 0.9554 (tpt) cc_final: 0.9184 (ppp) REVERT: B 461 PHE cc_start: 0.9528 (m-80) cc_final: 0.9305 (m-80) REVERT: B 468 PHE cc_start: 0.9042 (p90) cc_final: 0.8655 (p90) REVERT: B 494 PHE cc_start: 0.9272 (m-10) cc_final: 0.9049 (m-80) REVERT: B 547 PHE cc_start: 0.9514 (p90) cc_final: 0.9311 (p90) REVERT: A 171 LEU cc_start: 0.9779 (mt) cc_final: 0.9437 (tt) REVERT: A 178 PHE cc_start: 0.9347 (m-10) cc_final: 0.9131 (m-80) REVERT: A 250 MET cc_start: 0.9578 (tpt) cc_final: 0.9236 (ppp) REVERT: A 311 PHE cc_start: 0.9119 (m-80) cc_final: 0.8751 (m-80) REVERT: A 345 LEU cc_start: 0.9756 (pp) cc_final: 0.9538 (mt) REVERT: A 468 PHE cc_start: 0.9085 (p90) cc_final: 0.8792 (p90) REVERT: A 494 PHE cc_start: 0.9277 (m-10) cc_final: 0.9020 (m-80) REVERT: A 532 LEU cc_start: 0.9172 (tp) cc_final: 0.8957 (tp) REVERT: A 559 MET cc_start: 0.9712 (ptm) cc_final: 0.8944 (ppp) REVERT: A 560 MET cc_start: 0.9882 (mpp) cc_final: 0.9332 (mpp) REVERT: A 653 GLU cc_start: 0.9418 (mt-10) cc_final: 0.9200 (mm-30) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1614 time to fit residues: 40.8635 Evaluate side-chains 131 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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: 0.9990 chunk 45 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9504 Z= 0.202 Angle : 0.788 11.472 12914 Z= 0.388 Chirality : 0.044 0.168 1526 Planarity : 0.005 0.048 1580 Dihedral : 5.794 44.974 1262 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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: 0.78 (0.19), residues: 756 sheet: -1.01 (0.97), residues: 20 loop : -3.11 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 469 HIS 0.008 0.001 HIS A 847 PHE 0.026 0.002 PHE A 547 TYR 0.018 0.002 TYR B 146 ARG 0.004 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 161 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 209 MET cc_start: 0.9556 (pmm) cc_final: 0.9129 (tmm) REVERT: B 250 MET cc_start: 0.9562 (tpt) cc_final: 0.9174 (ppp) REVERT: B 461 PHE cc_start: 0.9539 (m-80) cc_final: 0.9305 (m-80) REVERT: B 468 PHE cc_start: 0.9036 (p90) cc_final: 0.8679 (p90) REVERT: B 490 LEU cc_start: 0.9841 (pp) cc_final: 0.9628 (pp) REVERT: B 494 PHE cc_start: 0.9261 (m-10) cc_final: 0.9038 (m-80) REVERT: A 171 LEU cc_start: 0.9779 (mt) cc_final: 0.9431 (tt) REVERT: A 178 PHE cc_start: 0.9363 (m-10) cc_final: 0.9128 (m-80) REVERT: A 250 MET cc_start: 0.9579 (tpt) cc_final: 0.9227 (ppp) REVERT: A 311 PHE cc_start: 0.9110 (m-80) cc_final: 0.8732 (m-80) REVERT: A 345 LEU cc_start: 0.9755 (pp) cc_final: 0.9550 (mt) REVERT: A 461 PHE cc_start: 0.9550 (m-80) cc_final: 0.9338 (m-80) REVERT: A 468 PHE cc_start: 0.9060 (p90) cc_final: 0.8695 (p90) REVERT: A 494 PHE cc_start: 0.9196 (m-10) cc_final: 0.8932 (m-80) REVERT: A 559 MET cc_start: 0.9707 (ptm) cc_final: 0.8959 (ppp) REVERT: A 560 MET cc_start: 0.9868 (mpp) cc_final: 0.9294 (mpp) REVERT: A 653 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9182 (mm-30) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1659 time to fit residues: 40.0887 Evaluate side-chains 122 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 0.1980 chunk 63 optimal weight: 8.9990 chunk 46 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.5094 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= 0.197 Angle : 0.792 10.247 12914 Z= 0.393 Chirality : 0.044 0.163 1526 Planarity : 0.005 0.050 1580 Dihedral : 5.712 45.050 1262 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: 758 sheet: -0.74 (0.95), residues: 20 loop : -3.03 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 469 HIS 0.006 0.001 HIS A 847 PHE 0.034 0.002 PHE B 306 TYR 0.015 0.001 TYR A 146 ARG 0.003 0.000 ARG A 663 *********************** REFINEMENT MACRO_CYCLE 9 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 165 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.047 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: B 178 PHE cc_start: 0.9583 (m-80) cc_final: 0.9273 (m-80) REVERT: B 209 MET cc_start: 0.9554 (pmm) cc_final: 0.9127 (tmm) REVERT: B 250 MET cc_start: 0.9556 (tpt) cc_final: 0.9136 (ppp) REVERT: B 490 LEU cc_start: 0.9843 (pp) cc_final: 0.9640 (pp) REVERT: B 494 PHE cc_start: 0.9277 (m-10) cc_final: 0.9017 (m-80) REVERT: B 547 PHE cc_start: 0.9581 (p90) cc_final: 0.9279 (p90) REVERT: B 559 MET cc_start: 0.9739 (ptm) cc_final: 0.9493 (ptm) REVERT: A 250 MET cc_start: 0.9584 (tpt) cc_final: 0.9222 (ppp) REVERT: A 311 PHE cc_start: 0.9116 (m-80) cc_final: 0.8723 (m-80) REVERT: A 345 LEU cc_start: 0.9745 (pp) cc_final: 0.9541 (mt) REVERT: A 461 PHE cc_start: 0.9550 (m-80) cc_final: 0.9342 (m-10) REVERT: A 494 PHE cc_start: 0.9225 (m-10) cc_final: 0.8979 (m-80) REVERT: A 527 ILE cc_start: 0.9194 (pt) cc_final: 0.8971 (pt) REVERT: A 532 LEU cc_start: 0.9097 (tp) cc_final: 0.8861 (tp) REVERT: A 559 MET cc_start: 0.9709 (ptm) cc_final: 0.9321 (ptp) REVERT: A 653 GLU cc_start: 0.9416 (mt-10) cc_final: 0.9188 (mm-30) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1727 time to fit residues: 42.3430 Evaluate side-chains 123 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.0470 chunk 53 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 9 optimal weight: 0.0670 chunk 72 optimal weight: 5.9990 chunk 57 optimal weight: 0.1980 chunk 74 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9504 Z= 0.194 Angle : 0.808 10.694 12914 Z= 0.402 Chirality : 0.045 0.186 1526 Planarity : 0.005 0.048 1580 Dihedral : 5.541 43.410 1262 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -0.63 (0.24), residues: 1182 helix: 0.89 (0.19), residues: 746 sheet: -0.27 (0.92), residues: 20 loop : -2.97 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 469 HIS 0.006 0.001 HIS B 847 PHE 0.029 0.002 PHE B 288 TYR 0.014 0.001 TYR B 296 ARG 0.001 0.000 ARG A 669 ********************** REFINEMENT MACRO_CYCLE 10 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 : 1.103 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 209 MET cc_start: 0.9519 (pmm) cc_final: 0.9109 (tmm) REVERT: B 250 MET cc_start: 0.9562 (tpt) cc_final: 0.9137 (ppp) REVERT: B 345 LEU cc_start: 0.9786 (pt) cc_final: 0.9529 (mt) REVERT: B 461 PHE cc_start: 0.9458 (m-80) cc_final: 0.9231 (m-80) REVERT: B 490 LEU cc_start: 0.9829 (pp) cc_final: 0.9617 (pp) REVERT: B 494 PHE cc_start: 0.9246 (m-10) cc_final: 0.8998 (m-80) REVERT: B 504 MET cc_start: 0.9593 (tmm) cc_final: 0.9347 (ppp) REVERT: B 527 ILE cc_start: 0.9156 (pt) cc_final: 0.8954 (pt) REVERT: B 560 MET cc_start: 0.9902 (mpp) cc_final: 0.9567 (mpp) REVERT: B 609 MET cc_start: 0.8445 (pmm) cc_final: 0.8241 (pmm) REVERT: A 178 PHE cc_start: 0.9612 (m-80) cc_final: 0.9333 (m-80) REVERT: A 250 MET cc_start: 0.9585 (tpt) cc_final: 0.9237 (ppp) REVERT: A 283 LEU cc_start: 0.9677 (pt) cc_final: 0.9437 (pt) REVERT: A 311 PHE cc_start: 0.9154 (m-80) cc_final: 0.8677 (m-80) REVERT: A 461 PHE cc_start: 0.9526 (m-80) cc_final: 0.9280 (m-80) REVERT: A 464 PHE cc_start: 0.9030 (p90) cc_final: 0.8747 (p90) REVERT: A 468 PHE cc_start: 0.8836 (p90) cc_final: 0.8530 (p90) REVERT: A 490 LEU cc_start: 0.9794 (pp) cc_final: 0.9542 (pp) REVERT: A 494 PHE cc_start: 0.9210 (m-10) cc_final: 0.8826 (m-80) REVERT: A 527 ILE cc_start: 0.9153 (pt) cc_final: 0.8937 (pt) REVERT: A 532 LEU cc_start: 0.9097 (tp) cc_final: 0.8766 (tp) REVERT: A 560 MET cc_start: 0.9888 (mpp) cc_final: 0.9546 (mpp) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1728 time to fit residues: 44.5013 Evaluate side-chains 132 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.0670 chunk 86 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 0.0970 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.051219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.040597 restraints weight = 75175.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.041875 restraints weight = 50114.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.042818 restraints weight = 36920.491| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.5644 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= 0.201 Angle : 0.826 11.221 12914 Z= 0.410 Chirality : 0.046 0.236 1526 Planarity : 0.005 0.049 1580 Dihedral : 5.532 45.361 1262 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: -0.51 (0.24), residues: 1182 helix: 0.95 (0.19), residues: 746 sheet: -0.06 (0.96), residues: 20 loop : -2.86 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP A 469 HIS 0.005 0.001 HIS A 847 PHE 0.047 0.002 PHE B 547 TYR 0.012 0.001 TYR A 146 ARG 0.001 0.000 ARG B 669 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1815.42 seconds wall clock time: 33 minutes 47.52 seconds (2027.52 seconds total)