Starting phenix.real_space_refine on Thu Jul 2 22:02:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pm5_13521/07_2026/7pm5_13521.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pm5_13521/07_2026/7pm5_13521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pm5_13521/07_2026/7pm5_13521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pm5_13521/07_2026/7pm5_13521.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pm5_13521/07_2026/7pm5_13521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pm5_13521/07_2026/7pm5_13521.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7pm5_13521/07_2026/7pm5_13521.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pm5_13521/07_2026/7pm5_13521.cif" } resolution = 3.1 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 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= 0.001 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 6474 2.51 5 N 1727 2.21 5 O 1901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10171 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 6092 Classifications: {'peptide': 746} Link IDs: {'PTRANS': 27, 'TRANS': 718} Chain breaks: 4 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.42, per 1000 atoms: 0.24 Number of scatterers: 10171 At special positions: 0 Unit cell: (108.12, 140.98, 149.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 4 15.00 Mg 2 11.99 O 1901 8.00 N 1727 7.00 C 6474 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 - 3.00 Amino acid : True - 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 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 371.5 milliseconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2378 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 15 sheets defined 54.6% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.268A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.679A pdb=" N LEU A 77 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 116 through 119 removed outlier: 4.464A pdb=" N TYR A 119 " --> pdb=" O LEU A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.596A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.543A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.568A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 259 through 268 removed outlier: 4.170A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.618A pdb=" N LYS A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 4.170A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.933A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.870A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 376 removed outlier: 3.801A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.676A pdb=" N LEU A 486 " --> pdb=" O PRO A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'A' and resid 506 through 513 Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.835A pdb=" N LYS A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.570A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.565A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 653 removed outlier: 3.696A pdb=" N ALA A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.599A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 723 through 736 removed outlier: 3.946A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.640A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.182A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.556A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.744A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.840A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.777A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.706A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 319 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.542A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.922A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.591A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA2, first strand: chain 'B' and resid 103 through 105 Processing sheet with id=AA3, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.540A pdb=" N LEU A 38 " --> pdb=" O TYR A 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.534A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.257A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA9, first strand: chain 'A' and resid 700 through 703 Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.856A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.173A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 520 hydrogen bonds defined for protein. 1461 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: 1.71 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1741 1.32 - 1.45: 2708 1.45 - 1.57: 5830 1.57 - 1.69: 6 1.69 - 1.82: 102 Bond restraints: 10387 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.450 0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.202 0.061 2.00e-02 2.50e+03 9.41e+00 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.463 0.062 2.10e-02 2.27e+03 8.64e+00 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.370 -0.041 1.40e-02 5.10e+03 8.53e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 7.02e+00 ... (remaining 10382 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 13743 2.38 - 4.75: 245 4.75 - 7.13: 33 7.13 - 9.51: 6 9.51 - 11.88: 5 Bond angle restraints: 14032 Sorted by residual: angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 109.82 11.88 1.80e+00 3.09e-01 4.36e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.78 -4.78 1.10e+00 8.26e-01 1.89e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 102.06 8.04 1.90e+00 2.77e-01 1.79e+01 angle pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " pdb=" CZ2 TRP H 1 " ideal model delta sigma weight residual 122.40 118.26 4.14 1.00e+00 1.00e+00 1.72e+01 angle pdb=" N TYR A 113 " pdb=" CA TYR A 113 " pdb=" CB TYR A 113 " ideal model delta sigma weight residual 113.15 106.47 6.68 1.63e+00 3.76e-01 1.68e+01 ... (remaining 14027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.90: 6046 27.90 - 55.80: 173 55.80 - 83.71: 29 83.71 - 111.61: 6 111.61 - 139.51: 4 Dihedral angle restraints: 6258 sinusoidal: 2568 harmonic: 3690 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 79.51 -139.51 1 2.00e+01 2.50e-03 4.23e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 70.90 -130.90 1 2.00e+01 2.50e-03 3.97e+01 dihedral pdb=" O1B ADP A1902 " pdb=" O3A ADP A1902 " pdb=" PB ADP A1902 " pdb=" PA ADP A1902 " ideal model delta sinusoidal sigma weight residual -60.00 68.66 -128.66 1 2.00e+01 2.50e-03 3.90e+01 ... (remaining 6255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.020: 1530 1.020 - 2.040: 0 2.040 - 3.060: 0 3.060 - 4.081: 0 4.081 - 5.101: 2 Chirality restraints: 1532 Sorted by residual: chirality pdb=" CB DTH H 4 " pdb=" CA DTH H 4 " pdb=" OG1 DTH H 4 " pdb=" CG2 DTH H 4 " both_signs ideal model delta sigma weight residual False 2.55 -2.55 5.10 2.00e-01 2.50e+01 6.50e+02 chirality pdb=" CA DTH H 4 " pdb=" N DTH H 4 " pdb=" C DTH H 4 " pdb=" CB DTH H 4 " both_signs ideal model delta sigma weight residual False 2.53 -2.40 4.92 2.00e-01 2.50e+01 6.06e+02 chirality pdb=" CG LEU A 782 " pdb=" CB LEU A 782 " pdb=" CD1 LEU A 782 " pdb=" CD2 LEU A 782 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1529 not shown) Planarity restraints: 1793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 113 " -0.037 2.00e-02 2.50e+03 3.28e-02 2.15e+01 pdb=" CG TYR A 113 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR A 113 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR A 113 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 113 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 113 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 113 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR A 113 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 677 " 0.086 9.50e-02 1.11e+02 5.14e-02 1.54e+01 pdb=" NE ARG A 677 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A 677 " 0.065 2.00e-02 2.50e+03 pdb=" NH1 ARG A 677 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG A 677 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 88 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C HIS C 88 " 0.064 2.00e-02 2.50e+03 pdb=" O HIS C 88 " -0.024 2.00e-02 2.50e+03 pdb=" N THR C 89 " -0.022 2.00e-02 2.50e+03 ... (remaining 1790 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 11 2.37 - 3.00: 5345 3.00 - 3.63: 15039 3.63 - 4.27: 23012 4.27 - 4.90: 38725 Nonbonded interactions: 82132 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.732 3.620 nonbonded pdb="MG MG A1901 " pdb=" O1B ADP A1902 " model vdw 2.037 2.170 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.056 3.040 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.182 2.170 nonbonded pdb=" OD1 ASN C 128 " pdb=" NZ LYS C 359 " model vdw 2.194 3.120 ... (remaining 82127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.420 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 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 : 0.005 0.122 10389 Z= 0.218 Angle : 0.836 11.883 14038 Z= 0.483 Chirality : 0.188 5.101 1532 Planarity : 0.007 0.053 1791 Dihedral : 14.748 139.511 3874 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.09 % Allowed : 0.28 % Favored : 99.63 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.21), residues: 1236 helix: -1.48 (0.17), residues: 590 sheet: -0.25 (0.40), residues: 150 loop : 0.27 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.066 0.010 ARG A 677 TYR 0.069 0.006 TYR A 113 PHE 0.033 0.002 PHE B 19 TRP 0.034 0.003 TRP C 79 HIS 0.010 0.001 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.22 (10387) covalent geometry : angle 0.83152 / 0.48 (14032) hydrogen bonds : bond 0.14765 / 9.56 ( 518) hydrogen bonds : angle 7.10071 / 5.03 ( 1461) link_TRANS : bond 0.00922 / 0.48 ( 2) link_TRANS : angle 4.24354 / 3.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.7943 (mmp) cc_final: 0.7232 (ttt) REVERT: A 305 MET cc_start: 0.8785 (tpp) cc_final: 0.8037 (tpp) REVERT: C 299 MET cc_start: 0.9064 (mmp) cc_final: 0.8834 (mmt) outliers start: 1 outliers final: 1 residues processed: 133 average time/residue: 0.1125 time to fit residues: 20.7545 Evaluate side-chains 80 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.0040 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 30.0000 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 0.0770 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.7354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN A 191 ASN A 264 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS C 162 ASN C 225 ASN C 280 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.093889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.058521 restraints weight = 25135.148| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.38 r_work: 0.2722 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10389 Z= 0.160 Angle : 0.654 13.851 14038 Z= 0.336 Chirality : 0.045 0.281 1532 Planarity : 0.004 0.069 1791 Dihedral : 9.210 136.461 1398 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.02 % Allowed : 3.88 % Favored : 95.11 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.23), residues: 1236 helix: 0.52 (0.21), residues: 605 sheet: 0.30 (0.39), residues: 156 loop : 0.84 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 542 TYR 0.032 0.002 TYR A 113 PHE 0.021 0.002 PHE C 255 TRP 0.016 0.002 TRP C 79 HIS 0.017 0.001 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (10387) covalent geometry : angle 0.65415 / 0.34 (14032) hydrogen bonds : bond 0.04592 / 2.99 ( 518) hydrogen bonds : angle 5.21606 / 3.70 ( 1461) link_TRANS : bond 0.00262 / 0.13 ( 2) link_TRANS : angle 1.15655 / 0.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.6827 (m-80) cc_final: 0.6478 (m-80) REVERT: B 96 PHE cc_start: 0.7548 (m-80) cc_final: 0.7078 (m-10) REVERT: B 105 MET cc_start: 0.7792 (mmp) cc_final: 0.7154 (ttt) REVERT: A 305 MET cc_start: 0.8976 (tpp) cc_final: 0.8367 (tpp) REVERT: A 788 MET cc_start: 0.5466 (mtt) cc_final: 0.4774 (tpt) outliers start: 11 outliers final: 6 residues processed: 93 average time/residue: 0.0874 time to fit residues: 12.0071 Evaluate side-chains 79 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 91 optimal weight: 0.3980 chunk 114 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 418 HIS A 463 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.093564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.057890 restraints weight = 25300.684| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.45 r_work: 0.2716 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10389 Z= 0.142 Angle : 0.572 12.649 14038 Z= 0.292 Chirality : 0.043 0.271 1532 Planarity : 0.004 0.050 1791 Dihedral : 8.142 135.384 1397 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.92 % Allowed : 5.26 % Favored : 93.81 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.24), residues: 1236 helix: 1.23 (0.22), residues: 604 sheet: 0.50 (0.39), residues: 161 loop : 0.76 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 343 TYR 0.018 0.001 TYR A 113 PHE 0.019 0.001 PHE C 255 TRP 0.013 0.001 TRP C 79 HIS 0.011 0.001 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (10387) covalent geometry : angle 0.57242 / 0.29 (14032) hydrogen bonds : bond 0.03916 / 2.55 ( 518) hydrogen bonds : angle 4.72075 / 3.35 ( 1461) link_TRANS : bond 0.00146 / 0.08 ( 2) link_TRANS : angle 0.55853 / 0.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.6889 (m-80) cc_final: 0.6569 (m-80) REVERT: B 96 PHE cc_start: 0.7480 (m-80) cc_final: 0.7257 (m-10) REVERT: B 105 MET cc_start: 0.7898 (mmp) cc_final: 0.7326 (ttt) REVERT: A 135 MET cc_start: 0.9304 (mmm) cc_final: 0.8760 (mmm) REVERT: A 194 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8332 (pt0) REVERT: A 305 MET cc_start: 0.8894 (tpp) cc_final: 0.8448 (tpp) REVERT: A 503 MET cc_start: 0.8868 (mmm) cc_final: 0.8432 (mmt) REVERT: A 788 MET cc_start: 0.5313 (mtt) cc_final: 0.4855 (tpt) REVERT: C 225 ASN cc_start: 0.8718 (m-40) cc_final: 0.8420 (m110) REVERT: C 227 MET cc_start: 0.8511 (tpp) cc_final: 0.8282 (tpp) outliers start: 10 outliers final: 2 residues processed: 83 average time/residue: 0.0819 time to fit residues: 10.5875 Evaluate side-chains 73 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 353 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 96 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 106 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.092659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.057251 restraints weight = 25362.218| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.41 r_work: 0.2706 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10389 Z= 0.152 Angle : 0.558 11.083 14038 Z= 0.280 Chirality : 0.043 0.281 1532 Planarity : 0.004 0.057 1791 Dihedral : 7.585 134.792 1397 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.20 % Allowed : 6.00 % Favored : 92.80 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.24), residues: 1236 helix: 1.65 (0.22), residues: 597 sheet: 0.71 (0.41), residues: 149 loop : 0.64 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 779 TYR 0.012 0.001 TYR A 113 PHE 0.015 0.001 PHE A 708 TRP 0.013 0.001 TRP C 79 HIS 0.009 0.001 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (10387) covalent geometry : angle 0.55782 / 0.28 (14032) hydrogen bonds : bond 0.03738 / 2.43 ( 518) hydrogen bonds : angle 4.50337 / 3.20 ( 1461) link_TRANS : bond 0.00157 / 0.08 ( 2) link_TRANS : angle 0.29776 / 0.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.6885 (m-80) cc_final: 0.6596 (m-80) REVERT: B 96 PHE cc_start: 0.7642 (m-80) cc_final: 0.7386 (m-10) REVERT: B 105 MET cc_start: 0.7959 (mmp) cc_final: 0.7260 (ttt) REVERT: A 132 MET cc_start: 0.8627 (ttm) cc_final: 0.8251 (tpp) REVERT: A 135 MET cc_start: 0.9328 (mmm) cc_final: 0.8778 (mmm) REVERT: A 194 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8327 (pt0) REVERT: A 305 MET cc_start: 0.8912 (tpp) cc_final: 0.8508 (tpp) REVERT: A 503 MET cc_start: 0.8838 (mmm) cc_final: 0.8534 (mmm) REVERT: A 767 LEU cc_start: 0.9154 (tt) cc_final: 0.8888 (pp) REVERT: A 788 MET cc_start: 0.5100 (mtt) cc_final: 0.4877 (tpt) outliers start: 13 outliers final: 3 residues processed: 82 average time/residue: 0.0887 time to fit residues: 11.1351 Evaluate side-chains 71 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.092625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.057042 restraints weight = 25200.911| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 3.43 r_work: 0.2695 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10389 Z= 0.147 Angle : 0.535 9.738 14038 Z= 0.268 Chirality : 0.042 0.249 1532 Planarity : 0.004 0.059 1791 Dihedral : 7.328 133.862 1397 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.92 % Allowed : 6.74 % Favored : 92.34 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.24), residues: 1236 helix: 1.76 (0.22), residues: 598 sheet: 0.83 (0.41), residues: 147 loop : 0.57 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 542 TYR 0.011 0.001 TYR A 113 PHE 0.013 0.001 PHE C 255 TRP 0.011 0.001 TRP C 79 HIS 0.008 0.001 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (10387) covalent geometry : angle 0.53517 / 0.27 (14032) hydrogen bonds : bond 0.03563 / 2.31 ( 518) hydrogen bonds : angle 4.41946 / 3.14 ( 1461) link_TRANS : bond 0.00149 / 0.08 ( 2) link_TRANS : angle 0.30997 / 0.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.6857 (m-80) cc_final: 0.6449 (m-80) REVERT: B 96 PHE cc_start: 0.7602 (m-80) cc_final: 0.7376 (m-10) REVERT: B 105 MET cc_start: 0.8054 (mmp) cc_final: 0.7353 (ttt) REVERT: B 148 ILE cc_start: 0.6136 (tt) cc_final: 0.5903 (pt) REVERT: A 132 MET cc_start: 0.8646 (ttm) cc_final: 0.8286 (tpp) REVERT: A 135 MET cc_start: 0.9350 (mmm) cc_final: 0.8857 (mmm) REVERT: A 194 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8293 (pt0) REVERT: A 305 MET cc_start: 0.8905 (tpp) cc_final: 0.8507 (tpp) REVERT: A 503 MET cc_start: 0.8828 (mmm) cc_final: 0.8559 (mmm) REVERT: A 767 LEU cc_start: 0.9170 (tt) cc_final: 0.8931 (pp) REVERT: A 788 MET cc_start: 0.5407 (mtt) cc_final: 0.5137 (tpp) outliers start: 10 outliers final: 5 residues processed: 82 average time/residue: 0.0787 time to fit residues: 10.1234 Evaluate side-chains 72 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain C residue 44 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 0.0870 chunk 95 optimal weight: 0.0570 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 238 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.093494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.057976 restraints weight = 25307.400| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.47 r_work: 0.2725 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10389 Z= 0.107 Angle : 0.523 9.688 14038 Z= 0.260 Chirality : 0.041 0.217 1532 Planarity : 0.003 0.053 1791 Dihedral : 7.068 130.734 1397 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.55 % Allowed : 7.94 % Favored : 91.51 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.24), residues: 1236 helix: 1.91 (0.22), residues: 597 sheet: 0.83 (0.41), residues: 147 loop : 0.55 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 779 TYR 0.010 0.001 TYR A 787 PHE 0.015 0.001 PHE C 255 TRP 0.010 0.001 TRP C 340 HIS 0.008 0.001 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (10387) covalent geometry : angle 0.52313 / 0.26 (14032) hydrogen bonds : bond 0.03278 / 2.13 ( 518) hydrogen bonds : angle 4.28109 / 3.04 ( 1461) link_TRANS : bond 0.00097 / 0.05 ( 2) link_TRANS : angle 0.23549 / 0.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 ASP cc_start: 0.6482 (t70) cc_final: 0.6147 (m-30) REVERT: B 93 PHE cc_start: 0.6882 (m-80) cc_final: 0.6586 (m-80) REVERT: B 96 PHE cc_start: 0.7558 (m-80) cc_final: 0.7308 (m-10) REVERT: B 105 MET cc_start: 0.8024 (mmp) cc_final: 0.7357 (ttt) REVERT: A 102 TYR cc_start: 0.8325 (m-80) cc_final: 0.7693 (m-80) REVERT: A 135 MET cc_start: 0.9353 (mmm) cc_final: 0.8870 (mmm) REVERT: A 194 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8341 (pt0) REVERT: A 305 MET cc_start: 0.8913 (tpp) cc_final: 0.8552 (tpp) REVERT: A 503 MET cc_start: 0.8791 (mmm) cc_final: 0.8519 (mmm) REVERT: A 767 LEU cc_start: 0.9194 (tt) cc_final: 0.8951 (pp) REVERT: C 176 MET cc_start: 0.9122 (mmt) cc_final: 0.8815 (mmt) REVERT: C 286 ASP cc_start: 0.8184 (t0) cc_final: 0.7957 (t0) outliers start: 6 outliers final: 3 residues processed: 82 average time/residue: 0.0761 time to fit residues: 9.9262 Evaluate side-chains 74 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 424 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 119 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 775 GLN ** 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 = 0.3616 r_free = 0.3616 target = 0.092816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.057278 restraints weight = 25008.639| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.42 r_work: 0.2712 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10389 Z= 0.133 Angle : 0.536 8.553 14038 Z= 0.267 Chirality : 0.041 0.184 1532 Planarity : 0.003 0.046 1791 Dihedral : 6.996 126.648 1397 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.65 % Allowed : 8.49 % Favored : 90.86 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.24), residues: 1236 helix: 1.94 (0.22), residues: 597 sheet: 0.93 (0.42), residues: 146 loop : 0.53 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 64 TYR 0.010 0.001 TYR A 787 PHE 0.013 0.001 PHE C 255 TRP 0.009 0.001 TRP C 340 HIS 0.008 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (10387) covalent geometry : angle 0.53654 / 0.27 (14032) hydrogen bonds : bond 0.03373 / 2.19 ( 518) hydrogen bonds : angle 4.25490 / 3.02 ( 1461) link_TRANS : bond 0.00136 / 0.07 ( 2) link_TRANS : angle 0.18034 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.8073 (mmp) cc_final: 0.7419 (ttt) REVERT: A 194 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8304 (pt0) REVERT: A 305 MET cc_start: 0.8959 (tpp) cc_final: 0.8612 (tpp) REVERT: A 503 MET cc_start: 0.8868 (mmm) cc_final: 0.8604 (mmm) REVERT: A 671 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.8182 (m-80) REVERT: A 767 LEU cc_start: 0.9194 (tt) cc_final: 0.8976 (pp) REVERT: C 176 MET cc_start: 0.9150 (mmt) cc_final: 0.8860 (mmt) outliers start: 7 outliers final: 5 residues processed: 79 average time/residue: 0.0791 time to fit residues: 9.8807 Evaluate side-chains 73 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 671 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 65 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 26 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 118 optimal weight: 0.0040 chunk 104 optimal weight: 0.8980 chunk 116 optimal weight: 0.5980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.093186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.057627 restraints weight = 25132.460| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.41 r_work: 0.2717 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10389 Z= 0.121 Angle : 0.532 7.674 14038 Z= 0.264 Chirality : 0.041 0.176 1532 Planarity : 0.003 0.047 1791 Dihedral : 6.888 124.044 1397 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.74 % Allowed : 8.59 % Favored : 90.67 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.24), residues: 1236 helix: 2.05 (0.22), residues: 596 sheet: 0.95 (0.42), residues: 146 loop : 0.49 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 64 TYR 0.009 0.001 TYR A 456 PHE 0.015 0.001 PHE B 96 TRP 0.013 0.001 TRP A 781 HIS 0.007 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (10387) covalent geometry : angle 0.53170 / 0.26 (14032) hydrogen bonds : bond 0.03310 / 2.15 ( 518) hydrogen bonds : angle 4.21049 / 2.99 ( 1461) link_TRANS : bond 0.00119 / 0.06 ( 2) link_TRANS : angle 0.17984 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.8079 (mmp) cc_final: 0.7414 (ttt) REVERT: A 135 MET cc_start: 0.9298 (mmm) cc_final: 0.8868 (mmm) REVERT: A 194 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8344 (pt0) REVERT: A 305 MET cc_start: 0.8961 (tpp) cc_final: 0.8619 (tpp) REVERT: A 503 MET cc_start: 0.8877 (mmm) cc_final: 0.8617 (mmm) REVERT: A 671 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.8132 (m-80) REVERT: A 751 PHE cc_start: 0.8124 (m-10) cc_final: 0.7814 (m-10) REVERT: A 767 LEU cc_start: 0.9207 (tt) cc_final: 0.8993 (pp) REVERT: C 176 MET cc_start: 0.9145 (mmt) cc_final: 0.8854 (mmt) outliers start: 8 outliers final: 6 residues processed: 79 average time/residue: 0.0879 time to fit residues: 10.8078 Evaluate side-chains 76 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 236 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 9 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.092737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.057202 restraints weight = 25158.750| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.42 r_work: 0.2704 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10389 Z= 0.138 Angle : 0.545 8.208 14038 Z= 0.269 Chirality : 0.041 0.178 1532 Planarity : 0.003 0.046 1791 Dihedral : 6.840 120.262 1397 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.92 % Allowed : 8.77 % Favored : 90.30 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.24), residues: 1236 helix: 2.07 (0.22), residues: 597 sheet: 0.94 (0.42), residues: 146 loop : 0.45 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 290 TYR 0.009 0.001 TYR A 456 PHE 0.013 0.001 PHE C 255 TRP 0.012 0.001 TRP A 781 HIS 0.007 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (10387) covalent geometry : angle 0.54523 / 0.27 (14032) hydrogen bonds : bond 0.03419 / 2.23 ( 518) hydrogen bonds : angle 4.21111 / 3.00 ( 1461) link_TRANS : bond 0.00140 / 0.07 ( 2) link_TRANS : angle 0.17586 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: B 105 MET cc_start: 0.8042 (mmp) cc_final: 0.7354 (ttt) REVERT: A 135 MET cc_start: 0.9326 (mmm) cc_final: 0.8925 (ttm) REVERT: A 194 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8345 (pt0) REVERT: A 305 MET cc_start: 0.8978 (tpp) cc_final: 0.8597 (tpp) REVERT: A 503 MET cc_start: 0.8891 (mmm) cc_final: 0.8624 (mmm) REVERT: A 751 PHE cc_start: 0.8124 (m-10) cc_final: 0.7808 (m-10) REVERT: A 767 LEU cc_start: 0.9186 (tt) cc_final: 0.8972 (pp) REVERT: C 176 MET cc_start: 0.9138 (mmt) cc_final: 0.8839 (mmt) outliers start: 10 outliers final: 8 residues processed: 77 average time/residue: 0.0811 time to fit residues: 10.0150 Evaluate side-chains 76 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 236 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 63 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.092650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.057289 restraints weight = 24831.394| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.39 r_work: 0.2705 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10389 Z= 0.138 Angle : 0.560 8.570 14038 Z= 0.275 Chirality : 0.041 0.180 1532 Planarity : 0.003 0.049 1791 Dihedral : 6.782 118.316 1397 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.65 % Allowed : 9.33 % Favored : 90.03 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.24), residues: 1236 helix: 2.11 (0.22), residues: 597 sheet: 0.93 (0.42), residues: 146 loop : 0.40 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 290 TYR 0.009 0.001 TYR B 89 PHE 0.013 0.001 PHE C 255 TRP 0.013 0.001 TRP A 781 HIS 0.007 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (10387) covalent geometry : angle 0.56019 / 0.28 (14032) hydrogen bonds : bond 0.03420 / 2.22 ( 518) hydrogen bonds : angle 4.19681 / 2.99 ( 1461) link_TRANS : bond 0.00143 / 0.08 ( 2) link_TRANS : angle 0.14388 / 0.10 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: B 105 MET cc_start: 0.8054 (mmp) cc_final: 0.7329 (ttt) REVERT: A 135 MET cc_start: 0.9338 (mmm) cc_final: 0.8928 (ttm) REVERT: A 194 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8321 (pt0) REVERT: A 305 MET cc_start: 0.8956 (tpp) cc_final: 0.8567 (tpp) REVERT: A 503 MET cc_start: 0.8917 (mmm) cc_final: 0.8636 (mmm) REVERT: A 751 PHE cc_start: 0.8111 (m-10) cc_final: 0.7796 (m-10) REVERT: A 767 LEU cc_start: 0.9193 (tt) cc_final: 0.8970 (pp) REVERT: C 176 MET cc_start: 0.9130 (mmt) cc_final: 0.8858 (mmt) outliers start: 7 outliers final: 7 residues processed: 78 average time/residue: 0.0786 time to fit residues: 9.8052 Evaluate side-chains 77 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 236 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 95 optimal weight: 0.4980 chunk 119 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.092991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.057353 restraints weight = 25318.029| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.44 r_work: 0.2708 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10389 Z= 0.128 Angle : 0.560 8.702 14038 Z= 0.275 Chirality : 0.041 0.179 1532 Planarity : 0.003 0.048 1791 Dihedral : 6.695 116.175 1397 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.65 % Allowed : 9.60 % Favored : 89.75 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.24), residues: 1236 helix: 2.11 (0.22), residues: 600 sheet: 0.98 (0.43), residues: 146 loop : 0.42 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 290 TYR 0.010 0.001 TYR A 787 PHE 0.012 0.001 PHE C 255 TRP 0.014 0.001 TRP A 781 HIS 0.007 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (10387) covalent geometry : angle 0.56007 / 0.28 (14032) hydrogen bonds : bond 0.03334 / 2.17 ( 518) hydrogen bonds : angle 4.18898 / 2.99 ( 1461) link_TRANS : bond 0.00125 / 0.07 ( 2) link_TRANS : angle 0.13448 / 0.10 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3009.71 seconds wall clock time: 52 minutes 19.43 seconds (3139.43 seconds total)