Starting phenix.real_space_refine on Mon Jul 28 17:01:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pm5_13521/07_2025/7pm5_13521.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pm5_13521/07_2025/7pm5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7pm5_13521/07_2025/7pm5_13521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pm5_13521/07_2025/7pm5_13521.map" model { file = "/net/cci-nas-00/data/ceres_data/7pm5_13521/07_2025/7pm5_13521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pm5_13521/07_2025/7pm5_13521.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} 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 Unresolved non-hydrogen dihedrals: 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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} 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: 6.83, per 1000 atoms: 0.67 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: 2.59 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.29 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: 3.54 Time building geometry restraints manager: 3.06 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: 6048 27.90 - 55.80: 181 55.80 - 83.71: 29 83.71 - 111.61: 6 111.61 - 139.51: 4 Dihedral angle restraints: 6268 sinusoidal: 2578 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 6265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1162 0.053 - 0.105: 295 0.105 - 0.158: 63 0.158 - 0.211: 9 0.211 - 0.264: 3 Chirality restraints: 1532 Sorted by residual: 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 chirality pdb=" CA PHE B 19 " pdb=" N PHE B 19 " pdb=" C PHE B 19 " pdb=" CB PHE B 19 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA CYS C 257 " pdb=" N CYS C 257 " pdb=" C CYS C 257 " pdb=" CB CYS C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.400 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 : 0.050 0.264 1532 Planarity : 0.007 0.053 1791 Dihedral : 14.893 139.511 3884 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 (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: -1.20 (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 TRP 0.034 0.003 TRP C 79 HIS 0.010 0.001 HIS B 147 PHE 0.033 0.002 PHE B 19 TYR 0.069 0.006 TYR A 113 ARG 0.066 0.010 ARG A 677 Details of bonding type rmsd link_TRANS : bond 0.00922 ( 2) link_TRANS : angle 4.24354 ( 6) hydrogen bonds : bond 0.14765 ( 518) hydrogen bonds : angle 7.10071 ( 1461) covalent geometry : bond 0.00454 (10387) covalent geometry : angle 0.83152 (14032) *********************** 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 : 1.121 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: 0.2575 time to fit residues: 47.2446 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 : 1.288 ------------------------------------------------------------------------------- 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 104 optimal weight: 0.8980 chunk 93 optimal weight: 0.0370 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 191 ASN A 264 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS C 59 GLN C 162 ASN C 225 ASN C 280 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.093949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.058594 restraints weight = 24929.183| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.41 r_work: 0.2723 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10389 Z= 0.158 Angle : 0.651 14.253 14038 Z= 0.333 Chirality : 0.045 0.300 1532 Planarity : 0.005 0.084 1791 Dihedral : 9.701 136.105 1408 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.20 % Allowed : 3.79 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.24), residues: 1236 helix: 0.53 (0.21), residues: 605 sheet: 0.17 (0.39), residues: 159 loop : 0.88 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 79 HIS 0.019 0.001 HIS B 147 PHE 0.024 0.001 PHE C 255 TYR 0.029 0.002 TYR A 113 ARG 0.005 0.001 ARG A 542 Details of bonding type rmsd link_TRANS : bond 0.00159 ( 2) link_TRANS : angle 0.92646 ( 6) hydrogen bonds : bond 0.04611 ( 518) hydrogen bonds : angle 5.17842 ( 1461) covalent geometry : bond 0.00354 (10387) covalent geometry : angle 0.65048 (14032) *********************** 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 98 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.6827 (m-80) cc_final: 0.6459 (m-80) REVERT: B 96 PHE cc_start: 0.7533 (m-80) cc_final: 0.7150 (m-10) REVERT: B 105 MET cc_start: 0.7733 (mmp) cc_final: 0.7125 (ttt) REVERT: A 305 MET cc_start: 0.8970 (tpp) cc_final: 0.8377 (tpp) REVERT: A 788 MET cc_start: 0.5499 (mtt) cc_final: 0.4820 (tpt) outliers start: 13 outliers final: 5 residues processed: 94 average time/residue: 0.3302 time to fit residues: 45.9671 Evaluate side-chains 78 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 3.335 ------------------------------------------------------------------------------- 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 257 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS A 463 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.092881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.057251 restraints weight = 25289.103| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.40 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: 0.8353 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10389 Z= 0.160 Angle : 0.581 12.501 14038 Z= 0.296 Chirality : 0.043 0.255 1532 Planarity : 0.004 0.050 1791 Dihedral : 8.692 136.065 1407 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.11 % Allowed : 5.08 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.24), residues: 1236 helix: 1.21 (0.22), residues: 604 sheet: 0.50 (0.39), residues: 161 loop : 0.74 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 79 HIS 0.011 0.001 HIS B 147 PHE 0.018 0.001 PHE C 255 TYR 0.018 0.001 TYR A 113 ARG 0.007 0.000 ARG A 343 Details of bonding type rmsd link_TRANS : bond 0.00171 ( 2) link_TRANS : angle 1.08760 ( 6) hydrogen bonds : bond 0.04035 ( 518) hydrogen bonds : angle 4.69921 ( 1461) covalent geometry : bond 0.00368 (10387) covalent geometry : angle 0.58036 (14032) *********************** 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 89 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.6893 (m-80) cc_final: 0.6590 (m-80) REVERT: B 105 MET cc_start: 0.7909 (mmp) cc_final: 0.7281 (ttt) REVERT: A 135 MET cc_start: 0.9315 (mmm) cc_final: 0.8771 (mmm) REVERT: A 194 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8337 (pt0) REVERT: A 305 MET cc_start: 0.8900 (tpp) cc_final: 0.8426 (tpp) REVERT: A 503 MET cc_start: 0.8868 (mmm) cc_final: 0.8416 (mmt) REVERT: A 767 LEU cc_start: 0.9139 (tp) cc_final: 0.8844 (pp) REVERT: A 788 MET cc_start: 0.5386 (mtt) cc_final: 0.4944 (tpt) REVERT: C 225 ASN cc_start: 0.8723 (m-40) cc_final: 0.8423 (m110) REVERT: C 227 MET cc_start: 0.8522 (tpp) cc_final: 0.8298 (tpp) REVERT: C 283 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8816 (mmm) outliers start: 12 outliers final: 4 residues processed: 85 average time/residue: 0.1997 time to fit residues: 26.3025 Evaluate side-chains 75 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 28 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 75 optimal weight: 0.0030 chunk 30 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3632 r_free = 0.3632 target = 0.093609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.058442 restraints weight = 25028.093| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.42 r_work: 0.2732 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10389 Z= 0.118 Angle : 0.537 11.166 14038 Z= 0.270 Chirality : 0.042 0.292 1532 Planarity : 0.004 0.056 1791 Dihedral : 8.038 135.563 1407 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.29 % Allowed : 5.82 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.24), residues: 1236 helix: 1.66 (0.22), residues: 595 sheet: 0.83 (0.41), residues: 147 loop : 0.65 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.009 0.001 HIS B 147 PHE 0.012 0.001 PHE C 255 TYR 0.011 0.001 TYR A 787 ARG 0.008 0.000 ARG A 779 Details of bonding type rmsd link_TRANS : bond 0.00189 ( 2) link_TRANS : angle 1.02559 ( 6) hydrogen bonds : bond 0.03487 ( 518) hydrogen bonds : angle 4.44032 ( 1461) covalent geometry : bond 0.00265 (10387) covalent geometry : angle 0.53640 (14032) *********************** 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 89 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.8012 (mmp) cc_final: 0.7338 (ttt) REVERT: A 132 MET cc_start: 0.8568 (ttm) cc_final: 0.8171 (tpp) REVERT: A 135 MET cc_start: 0.9333 (mmm) cc_final: 0.8772 (mmm) REVERT: A 194 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8301 (pt0) REVERT: A 305 MET cc_start: 0.8908 (tpp) cc_final: 0.8507 (tpp) REVERT: A 503 MET cc_start: 0.8775 (mmm) cc_final: 0.8452 (mmm) REVERT: A 767 LEU cc_start: 0.9156 (tp) cc_final: 0.8859 (pp) REVERT: A 788 MET cc_start: 0.5164 (mtt) cc_final: 0.4948 (tpt) REVERT: C 225 ASN cc_start: 0.8732 (m-40) cc_final: 0.8466 (m110) outliers start: 14 outliers final: 4 residues processed: 86 average time/residue: 0.2905 time to fit residues: 37.6313 Evaluate side-chains 75 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 10 optimal weight: 9.9990 chunk 37 optimal weight: 0.4980 chunk 115 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 70 optimal weight: 0.0030 chunk 41 optimal weight: 0.1980 chunk 15 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3637 r_free = 0.3637 target = 0.093878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.058527 restraints weight = 24915.626| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.42 r_work: 0.2733 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10389 Z= 0.113 Angle : 0.524 10.266 14038 Z= 0.260 Chirality : 0.041 0.233 1532 Planarity : 0.004 0.059 1791 Dihedral : 7.649 132.710 1407 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.02 % Allowed : 6.37 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.24), residues: 1236 helix: 1.83 (0.22), residues: 597 sheet: 0.86 (0.41), residues: 147 loop : 0.59 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.007 0.001 HIS B 147 PHE 0.012 0.001 PHE C 255 TYR 0.011 0.001 TYR A 387 ARG 0.002 0.000 ARG A 779 Details of bonding type rmsd link_TRANS : bond 0.00171 ( 2) link_TRANS : angle 0.92705 ( 6) hydrogen bonds : bond 0.03333 ( 518) hydrogen bonds : angle 4.32166 ( 1461) covalent geometry : bond 0.00253 (10387) covalent geometry : angle 0.52401 (14032) *********************** 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 90 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.8055 (mmp) cc_final: 0.7356 (ttt) REVERT: B 148 ILE cc_start: 0.6154 (tt) cc_final: 0.5939 (pt) REVERT: A 132 MET cc_start: 0.8606 (ttm) cc_final: 0.8216 (tpp) REVERT: A 135 MET cc_start: 0.9327 (mmm) cc_final: 0.8875 (mmm) REVERT: A 194 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8317 (pt0) REVERT: A 305 MET cc_start: 0.8891 (tpp) cc_final: 0.8536 (tpp) REVERT: A 503 MET cc_start: 0.8746 (mmm) cc_final: 0.8458 (mmm) REVERT: A 767 LEU cc_start: 0.9159 (tp) cc_final: 0.8884 (pp) REVERT: A 788 MET cc_start: 0.5399 (mtt) cc_final: 0.5169 (tpt) REVERT: C 176 MET cc_start: 0.9111 (mmt) cc_final: 0.8785 (mmt) outliers start: 11 outliers final: 7 residues processed: 87 average time/residue: 0.2372 time to fit residues: 32.6320 Evaluate side-chains 78 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 PHE 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 257 CYS Chi-restraints excluded: chain H residue 5 CYS 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 51 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.093341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.057890 restraints weight = 25256.892| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.42 r_work: 0.2721 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10389 Z= 0.126 Angle : 0.529 9.493 14038 Z= 0.261 Chirality : 0.041 0.213 1532 Planarity : 0.004 0.060 1791 Dihedral : 7.444 129.489 1407 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.92 % Allowed : 7.57 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.24), residues: 1236 helix: 1.92 (0.22), residues: 599 sheet: 0.85 (0.41), residues: 147 loop : 0.61 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.008 0.001 HIS B 147 PHE 0.014 0.001 PHE C 255 TYR 0.009 0.001 TYR A 456 ARG 0.002 0.000 ARG C 254 Details of bonding type rmsd link_TRANS : bond 0.00174 ( 2) link_TRANS : angle 0.89260 ( 6) hydrogen bonds : bond 0.03351 ( 518) hydrogen bonds : angle 4.24843 ( 1461) covalent geometry : bond 0.00288 (10387) covalent geometry : angle 0.52876 (14032) *********************** 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 84 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 ASP cc_start: 0.6461 (t70) cc_final: 0.6204 (m-30) REVERT: B 105 MET cc_start: 0.8042 (mmp) cc_final: 0.7351 (ttt) REVERT: A 132 MET cc_start: 0.8691 (ttm) cc_final: 0.8458 (tpp) REVERT: A 194 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8332 (pt0) REVERT: A 305 MET cc_start: 0.8904 (tpp) cc_final: 0.8547 (tpp) REVERT: A 503 MET cc_start: 0.8779 (mmm) cc_final: 0.8482 (mmm) REVERT: A 767 LEU cc_start: 0.9178 (tp) cc_final: 0.8898 (pp) REVERT: A 788 MET cc_start: 0.5401 (mtt) cc_final: 0.5190 (tpt) REVERT: A 790 MET cc_start: -0.1279 (tpp) cc_final: -0.1670 (tmm) REVERT: C 176 MET cc_start: 0.9127 (mmt) cc_final: 0.8816 (mmt) REVERT: C 283 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8479 (mmm) REVERT: C 286 ASP cc_start: 0.8179 (t0) cc_final: 0.7948 (t0) outliers start: 10 outliers final: 6 residues processed: 82 average time/residue: 0.2390 time to fit residues: 29.9656 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 : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 PHE 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 283 MET Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 97 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.091228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.055700 restraints weight = 25508.839| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.40 r_work: 0.2665 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10389 Z= 0.209 Angle : 0.577 8.794 14038 Z= 0.288 Chirality : 0.043 0.187 1532 Planarity : 0.004 0.051 1791 Dihedral : 7.513 126.912 1407 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.11 % Allowed : 8.22 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.24), residues: 1236 helix: 1.80 (0.22), residues: 605 sheet: 0.85 (0.42), residues: 147 loop : 0.43 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.008 0.001 HIS C 275 PHE 0.015 0.001 PHE C 255 TYR 0.012 0.001 TYR C 143 ARG 0.005 0.000 ARG A 779 Details of bonding type rmsd link_TRANS : bond 0.00216 ( 2) link_TRANS : angle 0.88036 ( 6) hydrogen bonds : bond 0.03803 ( 518) hydrogen bonds : angle 4.35556 ( 1461) covalent geometry : bond 0.00482 (10387) covalent geometry : angle 0.57731 (14032) *********************** 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 84 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 1.314 Fit side-chains revert: symmetry clash REVERT: B 105 MET cc_start: 0.8080 (mmp) cc_final: 0.7414 (ttt) REVERT: A 62 LEU cc_start: 0.8680 (tp) cc_final: 0.8434 (tt) REVERT: A 132 MET cc_start: 0.8728 (ttm) cc_final: 0.8514 (tpp) REVERT: A 135 MET cc_start: 0.9355 (mmm) cc_final: 0.8979 (ttm) REVERT: A 194 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8309 (pt0) REVERT: A 305 MET cc_start: 0.8971 (tpp) cc_final: 0.8550 (tpp) REVERT: A 503 MET cc_start: 0.8914 (mmm) cc_final: 0.8634 (mmm) REVERT: A 767 LEU cc_start: 0.9180 (tp) cc_final: 0.8894 (pp) REVERT: C 176 MET cc_start: 0.9170 (mmt) cc_final: 0.8850 (mmt) outliers start: 12 outliers final: 9 residues processed: 81 average time/residue: 0.2304 time to fit residues: 29.9102 Evaluate side-chains 77 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 PHE 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 671 PHE Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 87 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.091377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.056165 restraints weight = 25257.881| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.36 r_work: 0.2676 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10389 Z= 0.181 Angle : 0.575 8.650 14038 Z= 0.286 Chirality : 0.042 0.183 1532 Planarity : 0.004 0.049 1791 Dihedral : 7.386 126.161 1407 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.02 % Allowed : 8.68 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.24), residues: 1236 helix: 1.93 (0.22), residues: 592 sheet: 0.85 (0.42), residues: 148 loop : 0.44 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 340 HIS 0.008 0.001 HIS C 275 PHE 0.013 0.001 PHE C 255 TYR 0.011 0.001 TYR A 787 ARG 0.003 0.000 ARG A 789 Details of bonding type rmsd link_TRANS : bond 0.00214 ( 2) link_TRANS : angle 0.87223 ( 6) hydrogen bonds : bond 0.03691 ( 518) hydrogen bonds : angle 4.34741 ( 1461) covalent geometry : bond 0.00420 (10387) covalent geometry : angle 0.57452 (14032) *********************** 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 85 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 1.473 Fit side-chains revert: symmetry clash REVERT: B 105 MET cc_start: 0.8082 (mmp) cc_final: 0.7355 (ttt) REVERT: A 132 MET cc_start: 0.8730 (ttm) cc_final: 0.8520 (tpp) REVERT: A 135 MET cc_start: 0.9367 (mmm) cc_final: 0.8998 (ttm) REVERT: A 194 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8327 (pt0) REVERT: A 305 MET cc_start: 0.8971 (tpp) cc_final: 0.8564 (tpp) REVERT: A 503 MET cc_start: 0.8919 (mmm) cc_final: 0.8651 (mmm) REVERT: A 767 LEU cc_start: 0.9187 (tp) cc_final: 0.8908 (pp) REVERT: C 176 MET cc_start: 0.9161 (mmt) cc_final: 0.8840 (mmt) REVERT: C 269 MET cc_start: 0.9090 (mtp) cc_final: 0.8882 (mtm) REVERT: C 286 ASP cc_start: 0.8157 (t0) cc_final: 0.7932 (t0) outliers start: 11 outliers final: 9 residues processed: 83 average time/residue: 0.2037 time to fit residues: 27.4048 Evaluate side-chains 80 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 PHE 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 572 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 103 optimal weight: 0.1980 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.091752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.056441 restraints weight = 25109.267| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 3.36 r_work: 0.2682 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10389 Z= 0.157 Angle : 0.579 10.755 14038 Z= 0.286 Chirality : 0.042 0.182 1532 Planarity : 0.003 0.048 1791 Dihedral : 7.263 125.068 1407 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.92 % Allowed : 9.33 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.24), residues: 1236 helix: 1.99 (0.22), residues: 592 sheet: 0.82 (0.42), residues: 148 loop : 0.41 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 781 HIS 0.008 0.001 HIS C 275 PHE 0.014 0.001 PHE B 19 TYR 0.011 0.001 TYR A 787 ARG 0.003 0.000 ARG C 372 Details of bonding type rmsd link_TRANS : bond 0.00194 ( 2) link_TRANS : angle 0.85286 ( 6) hydrogen bonds : bond 0.03613 ( 518) hydrogen bonds : angle 4.32465 ( 1461) covalent geometry : bond 0.00363 (10387) covalent geometry : angle 0.57887 (14032) *********************** 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 83 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 1.990 Fit side-chains revert: symmetry clash REVERT: B 105 MET cc_start: 0.8075 (mmp) cc_final: 0.7351 (ttt) REVERT: A 135 MET cc_start: 0.9371 (mmm) cc_final: 0.9004 (ttm) REVERT: A 194 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8316 (pt0) REVERT: A 305 MET cc_start: 0.8964 (tpp) cc_final: 0.8562 (tpp) REVERT: A 503 MET cc_start: 0.8918 (mmm) cc_final: 0.8659 (mmm) REVERT: A 751 PHE cc_start: 0.8176 (m-10) cc_final: 0.7867 (m-10) REVERT: A 767 LEU cc_start: 0.9192 (tp) cc_final: 0.8907 (pp) REVERT: C 176 MET cc_start: 0.9153 (mmt) cc_final: 0.8864 (mmt) REVERT: C 283 MET cc_start: 0.9023 (mmp) cc_final: 0.8785 (mmm) outliers start: 10 outliers final: 8 residues processed: 82 average time/residue: 0.2416 time to fit residues: 32.4096 Evaluate side-chains 81 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 572 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 101 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 92 optimal weight: 0.8980 chunk 31 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.092326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.057122 restraints weight = 25271.279| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.38 r_work: 0.2699 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10389 Z= 0.130 Angle : 0.571 10.101 14038 Z= 0.281 Chirality : 0.041 0.179 1532 Planarity : 0.003 0.047 1791 Dihedral : 7.094 123.595 1407 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.74 % Allowed : 9.33 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.24), residues: 1236 helix: 2.04 (0.22), residues: 591 sheet: 0.83 (0.42), residues: 148 loop : 0.41 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 781 HIS 0.007 0.001 HIS C 275 PHE 0.012 0.001 PHE C 255 TYR 0.011 0.001 TYR A 787 ARG 0.002 0.000 ARG B 64 Details of bonding type rmsd link_TRANS : bond 0.00180 ( 2) link_TRANS : angle 0.85053 ( 6) hydrogen bonds : bond 0.03466 ( 518) hydrogen bonds : angle 4.25841 ( 1461) covalent geometry : bond 0.00300 (10387) covalent geometry : angle 0.57062 (14032) ********************** 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 81 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 1.477 Fit side-chains revert: symmetry clash REVERT: B 105 MET cc_start: 0.8074 (mmp) cc_final: 0.7345 (ttt) REVERT: A 135 MET cc_start: 0.9361 (mmm) cc_final: 0.8983 (ttm) REVERT: A 194 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8290 (pt0) REVERT: A 305 MET cc_start: 0.8969 (tpp) cc_final: 0.8624 (tpp) REVERT: A 503 MET cc_start: 0.8912 (mmm) cc_final: 0.8654 (mmm) REVERT: A 751 PHE cc_start: 0.8169 (m-10) cc_final: 0.7838 (m-10) REVERT: A 767 LEU cc_start: 0.9196 (tp) cc_final: 0.8907 (pp) REVERT: C 176 MET cc_start: 0.9156 (mmt) cc_final: 0.8867 (mmt) REVERT: C 283 MET cc_start: 0.9013 (mmp) cc_final: 0.8749 (mmm) outliers start: 8 outliers final: 8 residues processed: 80 average time/residue: 0.2445 time to fit residues: 30.9702 Evaluate side-chains 80 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 2.472 ------------------------------------------------------------------------------- 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 478 MET Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 95 optimal weight: 0.0470 chunk 18 optimal weight: 0.0170 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 123 optimal weight: 0.0980 chunk 61 optimal weight: 0.1980 chunk 49 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 overall best weight: 0.2316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN ** C 161 HIS ** 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 = 0.3647 r_free = 0.3647 target = 0.094483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.059606 restraints weight = 24933.441| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.39 r_work: 0.2761 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10389 Z= 0.099 Angle : 0.551 8.871 14038 Z= 0.270 Chirality : 0.040 0.171 1532 Planarity : 0.003 0.047 1791 Dihedral : 6.736 120.162 1407 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.65 % Allowed : 9.42 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.25), residues: 1236 helix: 2.11 (0.22), residues: 593 sheet: 0.81 (0.43), residues: 148 loop : 0.45 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 781 HIS 0.006 0.001 HIS C 275 PHE 0.011 0.001 PHE C 255 TYR 0.010 0.001 TYR B 89 ARG 0.002 0.000 ARG A 327 Details of bonding type rmsd link_TRANS : bond 0.00174 ( 2) link_TRANS : angle 0.85339 ( 6) hydrogen bonds : bond 0.03054 ( 518) hydrogen bonds : angle 4.11957 ( 1461) covalent geometry : bond 0.00222 (10387) covalent geometry : angle 0.55084 (14032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7637.63 seconds wall clock time: 141 minutes 8.38 seconds (8468.38 seconds total)