Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 07:47:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvu_4657/04_2023/6qvu_4657.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvu_4657/04_2023/6qvu_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_4657/04_2023/6qvu_4657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvu_4657/04_2023/6qvu_4657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvu_4657/04_2023/6qvu_4657.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvu_4657/04_2023/6qvu_4657.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 5.05, per 1000 atoms: 0.54 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: 3.35 Conformation dependent library (CDL) restraints added in 1.4 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: 0.43 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: 2.47 Time building geometry restraints manager: 3.67 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: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 5.860 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 25.350 Find NCS groups from input model: 0.480 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.320 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 4 residues processed: 209 average time/residue: 0.1794 time to fit residues: 54.8509 Evaluate side-chains 123 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0940 time to fit residues: 2.0481 ------------------------------------------------------------------------------- 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: 7.9990 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 92 optimal weight: 0.7980 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: 2.3764 ------------------------------------------------------------------------------- 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 369 HIS A 379 HIS A 436 HIS A 451 HIS A 838 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 9504 Z= 0.234 Angle : 0.818 13.267 12914 Z= 0.430 Chirality : 0.045 0.173 1526 Planarity : 0.007 0.053 1580 Dihedral : 7.094 51.089 1262 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer Outliers : 0.00 % 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: -2.64 (0.22), residues: 1182 helix: -0.81 (0.18), residues: 780 sheet: -1.74 (1.06), residues: 20 loop : -3.69 (0.26), residues: 382 *********************** 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 : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1848 time to fit residues: 42.1087 Evaluate side-chains 111 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.149 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5454 ------------------------------------------------------------------------------- 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: 8.9990 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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: 0.7665 moved from start: 0.3322 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= 0.203 Angle : 0.774 11.735 12914 Z= 0.398 Chirality : 0.044 0.183 1526 Planarity : 0.006 0.051 1580 Dihedral : 6.642 49.523 1262 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer Outliers : 0.20 % 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: -1.96 (0.23), residues: 1182 helix: -0.24 (0.18), residues: 784 sheet: -1.33 (1.05), residues: 20 loop : -3.58 (0.26), residues: 378 *********************** 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 153 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 151 time to evaluate : 1.093 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: symmetry clash outliers start: 2 outliers final: 0 residues processed: 153 average time/residue: 0.1753 time to fit residues: 40.0365 Evaluate side-chains 109 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4664 ------------------------------------------------------------------------------- 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: 9.9990 chunk 55 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 102 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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** ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3840 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= 0.216 Angle : 0.774 14.392 12914 Z= 0.393 Chirality : 0.044 0.147 1526 Planarity : 0.006 0.049 1580 Dihedral : 6.324 48.023 1262 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer Outliers : 0.00 % 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: -1.61 (0.24), residues: 1182 helix: 0.04 (0.18), residues: 780 sheet: -1.34 (0.99), residues: 20 loop : -3.41 (0.27), residues: 382 *********************** 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 152 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1690 time to fit residues: 38.3925 Evaluate side-chains 104 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.004 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3652 ------------------------------------------------------------------------------- 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: 6.9990 chunk 64 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 HIS ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 HIS ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4255 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= 0.264 Angle : 0.811 15.989 12914 Z= 0.417 Chirality : 0.045 0.181 1526 Planarity : 0.006 0.048 1580 Dihedral : 6.376 47.140 1262 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 25.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer Outliers : 0.00 % 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: -1.59 (0.23), residues: 1182 helix: -0.01 (0.18), residues: 784 sheet: -1.34 (1.04), residues: 20 loop : -3.30 (0.28), residues: 378 *********************** 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 139 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1774 time to fit residues: 36.9962 Evaluate side-chains 94 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.143 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4843 ------------------------------------------------------------------------------- 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: 0.9980 chunk 102 optimal weight: 0.4980 chunk 22 optimal weight: 0.0370 chunk 66 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.0660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 662 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4494 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= 0.198 Angle : 0.791 11.984 12914 Z= 0.396 Chirality : 0.045 0.260 1526 Planarity : 0.005 0.046 1580 Dihedral : 6.112 45.463 1262 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer Outliers : 0.00 % 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: -1.19 (0.24), residues: 1182 helix: 0.35 (0.18), residues: 784 sheet: -1.09 (1.02), residues: 20 loop : -3.28 (0.28), residues: 378 *********************** 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 153 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1740 time to fit residues: 40.3414 Evaluate side-chains 110 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.108 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4589 ------------------------------------------------------------------------------- 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: 2.9990 chunk 65 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 69 optimal weight: 0.4980 chunk 52 optimal weight: 10.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 9504 Z= 0.245 Angle : 0.816 14.472 12914 Z= 0.412 Chirality : 0.045 0.170 1526 Planarity : 0.005 0.044 1580 Dihedral : 6.103 44.193 1262 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 23.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer Outliers : 0.00 % 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: 0.30 (0.18), residues: 782 sheet: -1.06 (1.04), residues: 20 loop : -3.33 (0.28), residues: 380 *********************** 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 149 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1782 time to fit residues: 40.1105 Evaluate side-chains 105 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4774 ------------------------------------------------------------------------------- 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: 3.9990 chunk 45 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4931 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= 0.194 Angle : 0.789 11.311 12914 Z= 0.394 Chirality : 0.045 0.153 1526 Planarity : 0.005 0.045 1580 Dihedral : 5.874 44.134 1262 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer Outliers : 0.00 % 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: -0.95 (0.24), residues: 1182 helix: 0.66 (0.19), residues: 756 sheet: -0.85 (1.01), residues: 20 loop : -3.22 (0.28), residues: 406 *********************** 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 158 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1976 time to fit residues: 47.4462 Evaluate side-chains 114 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4985 ------------------------------------------------------------------------------- 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: 7.9990 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 0.0270 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 0.0570 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.5166 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= 0.195 Angle : 0.813 10.676 12914 Z= 0.411 Chirality : 0.046 0.185 1526 Planarity : 0.005 0.044 1580 Dihedral : 5.719 42.905 1262 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer Outliers : 0.00 % 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: -0.87 (0.24), residues: 1182 helix: 0.72 (0.19), residues: 756 sheet: -0.86 (0.97), residues: 20 loop : -3.17 (0.27), residues: 406 *********************** 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 : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1751 time to fit residues: 43.5346 Evaluate side-chains 117 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.087 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5622 ------------------------------------------------------------------------------- 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: 0.0770 chunk 53 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 9 optimal weight: 0.0770 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.5477 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= 0.194 Angle : 0.814 10.695 12914 Z= 0.413 Chirality : 0.046 0.170 1526 Planarity : 0.005 0.043 1580 Dihedral : 5.658 45.627 1262 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer Outliers : 0.00 % 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: -0.81 (0.24), residues: 1182 helix: 0.73 (0.19), residues: 758 sheet: -0.90 (0.94), residues: 20 loop : -3.09 (0.28), residues: 404 ********************** 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 161 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.123 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 outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1812 time to fit residues: 43.9889 Evaluate side-chains 118 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.159 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4279 ------------------------------------------------------------------------------- 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: 9.9990 chunk 86 optimal weight: 0.0770 chunk 13 optimal weight: 9.9990 chunk 26 optimal weight: 0.0070 chunk 93 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 96 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.051693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.041529 restraints weight = 72648.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.042711 restraints weight = 49058.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.043600 restraints weight = 36591.293| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.5702 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= 0.188 Angle : 0.816 10.457 12914 Z= 0.412 Chirality : 0.046 0.154 1526 Planarity : 0.005 0.043 1580 Dihedral : 5.546 44.774 1262 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer Outliers : 0.00 % 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: -0.59 (0.24), residues: 1182 helix: 0.84 (0.19), residues: 750 sheet: -0.82 (0.91), residues: 20 loop : -2.80 (0.29), residues: 412 =============================================================================== Job complete usr+sys time: 1819.59 seconds wall clock time: 34 minutes 12.94 seconds (2052.94 seconds total)