Starting phenix.real_space_refine on Fri May 23 19:45:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sml_40590/05_2025/8sml_40590_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sml_40590/05_2025/8sml_40590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sml_40590/05_2025/8sml_40590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sml_40590/05_2025/8sml_40590.map" model { file = "/net/cci-nas-00/data/ceres_data/8sml_40590/05_2025/8sml_40590_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sml_40590/05_2025/8sml_40590_neut.cif" } resolution = 3.3 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= 0.007 sd= 0.441 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 Ca 6 9.91 5 S 78 5.16 5 C 7894 2.51 5 N 2068 2.21 5 O 2348 1.98 5 H 12234 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24628 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 8910 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 39, 'TRANS': 530} Chain breaks: 10 Chain: "B" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1573 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1828 Classifications: {'peptide': 121} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 8910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 8910 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 39, 'TRANS': 530} Chain breaks: 10 Chain: "E" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1573 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1828 Classifications: {'peptide': 121} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 13.30, per 1000 atoms: 0.54 Number of scatterers: 24628 At special positions: 0 Unit cell: (156.145, 122.745, 68.47, 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) Ca 6 19.99 S 78 16.00 O 2348 8.00 N 2068 7.00 C 7894 6.00 H 12234 1.00 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 Time building additional restraints: 5.78 Conformation dependent library (CDL) restraints added in 1.9 seconds 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2964 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 34 sheets defined 16.7% alpha, 36.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 164 through 168 removed outlier: 3.757A pdb=" N ASP A 168 " --> pdb=" O ASP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'A' and resid 317 through 330 Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 444 through 453 Processing helix chain 'A' and resid 454 through 458 Processing helix chain 'A' and resid 471 through 474 Processing helix chain 'A' and resid 494 through 507 Processing helix chain 'A' and resid 527 through 531 Processing helix chain 'A' and resid 532 through 558 removed outlier: 3.974A pdb=" N ASN A 549 " --> pdb=" O CYS A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 562 No H-bonds generated for 'chain 'A' and resid 560 through 562' Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 610 through 621 Processing helix chain 'A' and resid 622 through 624 No H-bonds generated for 'chain 'A' and resid 622 through 624' Processing helix chain 'A' and resid 657 through 661 Processing helix chain 'C' and resid 64 through 67 removed outlier: 3.628A pdb=" N LYS C 67 " --> pdb=" O ASP C 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 64 through 67' Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.757A pdb=" N ASP D 168 " --> pdb=" O ASP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 205 through 208 Processing helix chain 'D' and resid 317 through 330 Processing helix chain 'D' and resid 406 through 408 No H-bonds generated for 'chain 'D' and resid 406 through 408' Processing helix chain 'D' and resid 444 through 453 Processing helix chain 'D' and resid 454 through 458 Processing helix chain 'D' and resid 471 through 474 Processing helix chain 'D' and resid 494 through 507 Processing helix chain 'D' and resid 527 through 531 Processing helix chain 'D' and resid 532 through 558 removed outlier: 3.974A pdb=" N ASN D 549 " --> pdb=" O CYS D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 562 No H-bonds generated for 'chain 'D' and resid 560 through 562' Processing helix chain 'D' and resid 575 through 577 No H-bonds generated for 'chain 'D' and resid 575 through 577' Processing helix chain 'D' and resid 610 through 621 Processing helix chain 'D' and resid 622 through 624 No H-bonds generated for 'chain 'D' and resid 622 through 624' Processing helix chain 'D' and resid 657 through 661 Processing helix chain 'F' and resid 64 through 67 removed outlier: 3.627A pdb=" N LYS F 67 " --> pdb=" O ASP F 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 64 through 67' Processing helix chain 'F' and resid 89 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 removed outlier: 6.854A pdb=" N ILE A 7 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 20 removed outlier: 3.983A pdb=" N VAL A 104 " --> pdb=" O TYR A 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 20 removed outlier: 4.805A pdb=" N ASP A 248 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 213 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 148 through 150 removed outlier: 6.521A pdb=" N ALA A 148 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL A 283 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASP A 273 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU A 199 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 297 through 298 removed outlier: 8.084A pdb=" N VAL A 392 " --> pdb=" O PRO A 365 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL A 367 " --> pdb=" O VAL A 392 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 333 through 336 removed outlier: 6.385A pdb=" N GLN A 306 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR A 335 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL A 308 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG A 650 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL A 308 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN A 648 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 412 removed outlier: 6.325A pdb=" N ILE A 428 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU A 462 " --> pdb=" O ILE A 428 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE A 430 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 416 through 418 Processing sheet with id=AA9, first strand: chain 'A' and resid 476 through 480 removed outlier: 8.123A pdb=" N ILE A 565 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU A 489 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE A 567 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU A 491 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 571 through 573 Processing sheet with id=AB2, first strand: chain 'A' and resid 590 through 592 Processing sheet with id=AB3, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AB4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.542A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SER B 53 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.138A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 6 through 10 Processing sheet with id=AB7, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.189A pdb=" N GLY C 13 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE C 36 " --> pdb=" O SER C 52 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER C 52 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP C 38 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.189A pdb=" N GLY C 13 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 6 through 8 removed outlier: 6.854A pdb=" N ILE D 7 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 15 through 20 removed outlier: 3.983A pdb=" N VAL D 104 " --> pdb=" O TYR D 96 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 15 through 20 removed outlier: 4.804A pdb=" N ASP D 248 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL D 213 " --> pdb=" O VAL D 228 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 148 through 150 removed outlier: 6.521A pdb=" N ALA D 148 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL D 283 " --> pdb=" O ASP D 273 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASP D 273 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU D 199 " --> pdb=" O LEU D 238 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 297 through 298 removed outlier: 8.084A pdb=" N VAL D 392 " --> pdb=" O PRO D 365 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL D 367 " --> pdb=" O VAL D 392 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 333 through 336 removed outlier: 6.385A pdb=" N GLN D 306 " --> pdb=" O LYS D 333 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR D 335 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL D 308 " --> pdb=" O THR D 335 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG D 650 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL D 308 " --> pdb=" O ASN D 648 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN D 648 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 410 through 412 removed outlier: 6.326A pdb=" N ILE D 428 " --> pdb=" O VAL D 460 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU D 462 " --> pdb=" O ILE D 428 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE D 430 " --> pdb=" O LEU D 462 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 416 through 418 Processing sheet with id=AC8, first strand: chain 'D' and resid 476 through 480 removed outlier: 8.123A pdb=" N ILE D 565 " --> pdb=" O PHE D 487 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU D 489 " --> pdb=" O ILE D 565 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE D 567 " --> pdb=" O LEU D 489 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU D 491 " --> pdb=" O ILE D 567 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 571 through 573 Processing sheet with id=AD1, first strand: chain 'D' and resid 590 through 592 Processing sheet with id=AD2, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AD3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.542A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER E 53 " --> pdb=" O TYR E 49 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.139A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 6 through 10 Processing sheet with id=AD6, first strand: chain 'F' and resid 13 through 14 removed outlier: 6.188A pdb=" N GLY F 13 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE F 36 " --> pdb=" O SER F 52 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER F 52 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP F 38 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 13 through 14 removed outlier: 6.188A pdb=" N GLY F 13 " --> pdb=" O THR F 123 " (cutoff:3.500A) 494 hydrogen bonds defined for protein. 1230 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: 9.55 Time building geometry restraints manager: 7.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 12192 1.13 - 1.30: 2073 1.30 - 1.47: 5111 1.47 - 1.65: 5416 1.65 - 1.82: 114 Bond restraints: 24906 Sorted by residual: bond pdb=" N GLU D 556 " pdb=" H GLU D 556 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" NE2 HIS C 37 " pdb=" HE2 HIS C 37 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N ALA C 112 " pdb=" H ALA C 112 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N ASP B 82 " pdb=" H ASP B 82 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" CE1 TYR C 62 " pdb=" HE1 TYR C 62 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.73e+01 ... (remaining 24901 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 41135 2.50 - 5.01: 1955 5.01 - 7.51: 1867 7.51 - 10.01: 23 10.01 - 12.52: 8 Bond angle restraints: 44988 Sorted by residual: angle pdb=" CB HIS D 245 " pdb=" CG HIS D 245 " pdb=" CD2 HIS D 245 " ideal model delta sigma weight residual 131.20 125.34 5.86 1.30e+00 5.92e-01 2.03e+01 angle pdb=" CB HIS A 245 " pdb=" CG HIS A 245 " pdb=" CD2 HIS A 245 " ideal model delta sigma weight residual 131.20 125.37 5.83 1.30e+00 5.92e-01 2.01e+01 angle pdb=" C ASP A 369 " pdb=" N SER A 370 " pdb=" CA SER A 370 " ideal model delta sigma weight residual 120.60 127.44 -6.84 1.53e+00 4.27e-01 2.00e+01 angle pdb=" C ASP D 369 " pdb=" N SER D 370 " pdb=" CA SER D 370 " ideal model delta sigma weight residual 120.60 127.43 -6.83 1.53e+00 4.27e-01 1.99e+01 angle pdb=" O GLU D 170 " pdb=" C GLU D 170 " pdb=" N VAL D 171 " ideal model delta sigma weight residual 123.26 118.87 4.39 1.05e+00 9.07e-01 1.75e+01 ... (remaining 44983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 10804 18.00 - 36.00: 596 36.00 - 53.99: 236 53.99 - 71.99: 172 71.99 - 89.99: 36 Dihedral angle restraints: 11844 sinusoidal: 6424 harmonic: 5420 Sorted by residual: dihedral pdb=" CA LYS D 224 " pdb=" C LYS D 224 " pdb=" N CYS D 225 " pdb=" CA CYS D 225 " ideal model delta harmonic sigma weight residual 180.00 156.39 23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA LYS A 224 " pdb=" C LYS A 224 " pdb=" N CYS A 225 " pdb=" CA CYS A 225 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA PHE F 108 " pdb=" C PHE F 108 " pdb=" N TRP F 109 " pdb=" CA TRP F 109 " ideal model delta harmonic sigma weight residual -180.00 -156.76 -23.24 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 11841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1466 0.070 - 0.139: 363 0.139 - 0.209: 91 0.209 - 0.278: 8 0.278 - 0.348: 2 Chirality restraints: 1930 Sorted by residual: chirality pdb=" CA SER E 52 " pdb=" N SER E 52 " pdb=" C SER E 52 " pdb=" CB SER E 52 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA SER B 52 " pdb=" N SER B 52 " pdb=" C SER B 52 " pdb=" CB SER B 52 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA ASP A 169 " pdb=" N ASP A 169 " pdb=" C ASP A 169 " pdb=" CB ASP A 169 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1927 not shown) Planarity restraints: 3666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 111 " 0.108 2.00e-02 2.50e+03 5.69e-02 1.29e+02 pdb=" CG TRP C 111 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP C 111 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP C 111 " -0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP C 111 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP C 111 " -0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP C 111 " -0.057 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 111 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 111 " -0.028 2.00e-02 2.50e+03 pdb=" CH2 TRP C 111 " 0.031 2.00e-02 2.50e+03 pdb=" HD1 TRP C 111 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 TRP C 111 " -0.105 2.00e-02 2.50e+03 pdb=" HE3 TRP C 111 " -0.079 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 111 " 0.038 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 111 " -0.024 2.00e-02 2.50e+03 pdb=" HH2 TRP C 111 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 111 " -0.108 2.00e-02 2.50e+03 5.68e-02 1.29e+02 pdb=" CG TRP F 111 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP F 111 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP F 111 " 0.026 2.00e-02 2.50e+03 pdb=" NE1 TRP F 111 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP F 111 " 0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP F 111 " 0.057 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 111 " -0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 111 " 0.028 2.00e-02 2.50e+03 pdb=" CH2 TRP F 111 " -0.031 2.00e-02 2.50e+03 pdb=" HD1 TRP F 111 " -0.020 2.00e-02 2.50e+03 pdb=" HE1 TRP F 111 " 0.105 2.00e-02 2.50e+03 pdb=" HE3 TRP F 111 " 0.079 2.00e-02 2.50e+03 pdb=" HZ2 TRP F 111 " -0.038 2.00e-02 2.50e+03 pdb=" HZ3 TRP F 111 " 0.024 2.00e-02 2.50e+03 pdb=" HH2 TRP F 111 " -0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 212 " 0.062 9.50e-02 1.11e+02 7.01e-02 1.01e+02 pdb=" NE ARG D 212 " -0.044 2.00e-02 2.50e+03 pdb=" CZ ARG D 212 " -0.056 2.00e-02 2.50e+03 pdb=" NH1 ARG D 212 " -0.038 2.00e-02 2.50e+03 pdb=" NH2 ARG D 212 " -0.041 2.00e-02 2.50e+03 pdb="HH11 ARG D 212 " 0.056 2.00e-02 2.50e+03 pdb="HH12 ARG D 212 " 0.059 2.00e-02 2.50e+03 pdb="HH21 ARG D 212 " 0.139 2.00e-02 2.50e+03 pdb="HH22 ARG D 212 " -0.079 2.00e-02 2.50e+03 ... (remaining 3663 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 1456 2.14 - 2.75: 41601 2.75 - 3.37: 68209 3.37 - 3.98: 94788 3.98 - 4.60: 137827 Nonbonded interactions: 343881 Sorted by model distance: nonbonded pdb=" HG SER D 161 " pdb=" H ALA D 163 " model vdw 1.519 2.100 nonbonded pdb=" HG SER A 161 " pdb=" H ALA A 163 " model vdw 1.520 2.100 nonbonded pdb=" OD1 ASP A 258 " pdb=" H THR A 259 " model vdw 1.576 2.450 nonbonded pdb=" OD1 ASP D 258 " pdb=" H THR D 259 " model vdw 1.577 2.450 nonbonded pdb=" OD1 ASP C 75 " pdb=" HG SER C 77 " model vdw 1.595 2.450 ... (remaining 343876 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 9.330 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: 0.400 Extract box with map and model: 0.920 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 52.650 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 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 : 0.010 0.079 12672 Z= 0.570 Angle : 1.008 8.041 17196 Z= 0.650 Chirality : 0.064 0.348 1930 Planarity : 0.007 0.063 2196 Dihedral : 11.401 89.769 4608 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.08 % Favored : 97.80 % Rotamer: Outliers : 0.14 % Allowed : 1.30 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.50 (0.21), residues: 1542 helix: 0.12 (0.35), residues: 164 sheet: 0.42 (0.21), residues: 584 loop : 0.48 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.008 TRP C 111 HIS 0.009 0.001 HIS C 37 PHE 0.072 0.003 PHE E 98 TYR 0.073 0.007 TYR F 56 ARG 0.012 0.001 ARG D 212 Details of bonding type rmsd hydrogen bonds : bond 0.18060 ( 466) hydrogen bonds : angle 9.17544 ( 1230) covalent geometry : bond 0.00985 (12672) covalent geometry : angle 1.00802 (17196) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 349 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.7478 (mtp) cc_final: 0.7190 (mtt) REVERT: A 572 LYS cc_start: 0.7392 (pttt) cc_final: 0.7105 (pttm) REVERT: D 572 LYS cc_start: 0.7357 (pttt) cc_final: 0.7077 (pttm) outliers start: 2 outliers final: 0 residues processed: 349 average time/residue: 0.5481 time to fit residues: 275.5026 Evaluate side-chains 192 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** D 215 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 = 0.4421 r_free = 0.4421 target = 0.191001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.149759 restraints weight = 34647.035| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.56 r_work: 0.3873 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12672 Z= 0.188 Angle : 0.620 4.996 17196 Z= 0.339 Chirality : 0.047 0.188 1930 Planarity : 0.005 0.045 2196 Dihedral : 4.667 23.641 1686 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.66 % Allowed : 6.63 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.15 (0.21), residues: 1542 helix: 0.90 (0.38), residues: 168 sheet: 0.05 (0.20), residues: 608 loop : 0.12 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 49 HIS 0.010 0.001 HIS D 471 PHE 0.015 0.002 PHE D 285 TYR 0.012 0.002 TYR B 49 ARG 0.003 0.001 ARG D 495 Details of bonding type rmsd hydrogen bonds : bond 0.06091 ( 466) hydrogen bonds : angle 7.22871 ( 1230) covalent geometry : bond 0.00433 (12672) covalent geometry : angle 0.61961 (17196) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.7088 (mmp) cc_final: 0.6811 (mmm) REVERT: A 509 HIS cc_start: 0.7240 (m-70) cc_final: 0.6985 (m-70) REVERT: A 572 LYS cc_start: 0.7587 (pttt) cc_final: 0.7306 (pttm) REVERT: C 21 LEU cc_start: 0.6973 (tp) cc_final: 0.6676 (tp) REVERT: D 239 MET cc_start: 0.7084 (mmp) cc_final: 0.6802 (mmm) REVERT: D 509 HIS cc_start: 0.7196 (m-70) cc_final: 0.6935 (m-70) REVERT: D 572 LYS cc_start: 0.7512 (pttt) cc_final: 0.7207 (pttm) REVERT: F 21 LEU cc_start: 0.7029 (tp) cc_final: 0.6705 (tp) outliers start: 23 outliers final: 11 residues processed: 227 average time/residue: 0.5323 time to fit residues: 174.1686 Evaluate side-chains 189 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain E residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 124 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 chunk 117 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 245 HIS D 215 GLN D 245 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.184073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.142540 restraints weight = 35337.332| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.56 r_work: 0.3782 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12672 Z= 0.188 Angle : 0.599 4.694 17196 Z= 0.325 Chirality : 0.046 0.174 1930 Planarity : 0.005 0.047 2196 Dihedral : 4.600 21.041 1686 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.80 % Allowed : 8.14 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.09 (0.21), residues: 1542 helix: 1.29 (0.40), residues: 166 sheet: -0.22 (0.20), residues: 604 loop : -0.07 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 49 HIS 0.004 0.001 HIS D 471 PHE 0.015 0.002 PHE B 98 TYR 0.021 0.002 TYR E 49 ARG 0.004 0.001 ARG B 66 Details of bonding type rmsd hydrogen bonds : bond 0.05196 ( 466) hydrogen bonds : angle 6.73046 ( 1230) covalent geometry : bond 0.00433 (12672) covalent geometry : angle 0.59930 (17196) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.7117 (mmp) cc_final: 0.6844 (mmm) REVERT: A 329 LYS cc_start: 0.7606 (mttt) cc_final: 0.7194 (tptp) REVERT: D 239 MET cc_start: 0.7131 (mmp) cc_final: 0.6860 (mmm) REVERT: D 329 LYS cc_start: 0.7658 (mttt) cc_final: 0.7242 (tptp) REVERT: E 66 ARG cc_start: 0.7871 (ttt-90) cc_final: 0.7612 (ttt-90) outliers start: 25 outliers final: 13 residues processed: 220 average time/residue: 0.5376 time to fit residues: 169.1175 Evaluate side-chains 198 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 185 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 602 PHE Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain F residue 15 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 13 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 34 optimal weight: 0.0870 chunk 56 optimal weight: 0.2980 chunk 88 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 86 optimal weight: 0.0970 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 ASN D 438 ASN D 569 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.185689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.143146 restraints weight = 35636.297| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.67 r_work: 0.3786 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12672 Z= 0.113 Angle : 0.526 4.086 17196 Z= 0.281 Chirality : 0.044 0.167 1930 Planarity : 0.005 0.044 2196 Dihedral : 4.324 22.138 1686 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.73 % Allowed : 9.22 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.03 (0.21), residues: 1542 helix: 1.82 (0.40), residues: 166 sheet: -0.28 (0.20), residues: 604 loop : 0.03 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 49 HIS 0.003 0.001 HIS A 471 PHE 0.010 0.001 PHE C 108 TYR 0.013 0.001 TYR F 34 ARG 0.003 0.000 ARG C 100 Details of bonding type rmsd hydrogen bonds : bond 0.04256 ( 466) hydrogen bonds : angle 6.15529 ( 1230) covalent geometry : bond 0.00261 (12672) covalent geometry : angle 0.52566 (17196) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.7135 (mmp) cc_final: 0.6863 (mmm) REVERT: A 572 LYS cc_start: 0.7573 (pttt) cc_final: 0.7067 (pptt) REVERT: B 66 ARG cc_start: 0.7806 (ttt-90) cc_final: 0.7514 (ttt-90) REVERT: D 239 MET cc_start: 0.7145 (mmp) cc_final: 0.6876 (mmm) REVERT: E 66 ARG cc_start: 0.7838 (ttt-90) cc_final: 0.7562 (ttt-90) outliers start: 24 outliers final: 15 residues processed: 210 average time/residue: 0.5235 time to fit residues: 162.0355 Evaluate side-chains 197 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 602 PHE Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain E residue 20 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 14 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 140 optimal weight: 0.0970 chunk 137 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN D 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.178966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.137509 restraints weight = 36761.326| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.72 r_work: 0.3699 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12672 Z= 0.202 Angle : 0.603 4.933 17196 Z= 0.325 Chirality : 0.046 0.169 1930 Planarity : 0.006 0.049 2196 Dihedral : 4.678 20.382 1686 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.45 % Allowed : 8.79 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.49 (0.20), residues: 1542 helix: 1.41 (0.40), residues: 166 sheet: -0.50 (0.21), residues: 576 loop : -0.46 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 466 HIS 0.004 0.001 HIS A 471 PHE 0.016 0.002 PHE D 629 TYR 0.022 0.002 TYR B 49 ARG 0.003 0.001 ARG A 550 Details of bonding type rmsd hydrogen bonds : bond 0.04576 ( 466) hydrogen bonds : angle 6.16431 ( 1230) covalent geometry : bond 0.00483 (12672) covalent geometry : angle 0.60324 (17196) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 GLU cc_start: 0.7197 (tt0) cc_final: 0.6969 (tm-30) REVERT: A 239 MET cc_start: 0.7223 (mmp) cc_final: 0.6971 (mmm) REVERT: A 572 LYS cc_start: 0.7651 (pttt) cc_final: 0.7141 (pptt) REVERT: A 648 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7389 (m110) REVERT: D 80 MET cc_start: 0.4181 (mtm) cc_final: 0.2791 (tpt) REVERT: D 167 GLU cc_start: 0.7183 (tt0) cc_final: 0.6962 (tm-30) REVERT: D 239 MET cc_start: 0.7171 (mmp) cc_final: 0.6920 (mmm) REVERT: D 648 ASN cc_start: 0.7828 (OUTLIER) cc_final: 0.7451 (m110) outliers start: 34 outliers final: 23 residues processed: 206 average time/residue: 0.5135 time to fit residues: 160.6538 Evaluate side-chains 201 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 438 ASN Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain D residue 648 ASN Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 34 TYR Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 130 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 141 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN D 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.178856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.137776 restraints weight = 36556.648| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.64 r_work: 0.3702 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12672 Z= 0.180 Angle : 0.580 4.632 17196 Z= 0.312 Chirality : 0.045 0.164 1930 Planarity : 0.005 0.049 2196 Dihedral : 4.688 24.612 1686 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.74 % Allowed : 9.37 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.60 (0.20), residues: 1542 helix: 1.44 (0.41), residues: 166 sheet: -0.46 (0.21), residues: 582 loop : -0.66 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 658 HIS 0.003 0.001 HIS A 595 PHE 0.013 0.002 PHE E 98 TYR 0.017 0.002 TYR F 33 ARG 0.003 0.001 ARG A 427 Details of bonding type rmsd hydrogen bonds : bond 0.04270 ( 466) hydrogen bonds : angle 6.06078 ( 1230) covalent geometry : bond 0.00428 (12672) covalent geometry : angle 0.57966 (17196) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 GLU cc_start: 0.7188 (tt0) cc_final: 0.6985 (tm-30) REVERT: A 239 MET cc_start: 0.7198 (mmp) cc_final: 0.6953 (mmm) REVERT: A 572 LYS cc_start: 0.7743 (pttt) cc_final: 0.7226 (pptt) REVERT: A 648 ASN cc_start: 0.7787 (OUTLIER) cc_final: 0.7521 (m110) REVERT: C 14 LEU cc_start: 0.7917 (tt) cc_final: 0.7505 (mp) REVERT: C 45 LYS cc_start: 0.7025 (mmtt) cc_final: 0.6197 (mtpp) REVERT: C 100 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.5739 (ptp-170) REVERT: D 167 GLU cc_start: 0.7195 (tt0) cc_final: 0.6990 (tm-30) REVERT: D 239 MET cc_start: 0.7209 (mmp) cc_final: 0.6967 (mmm) REVERT: D 648 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7535 (m110) REVERT: E 79 GLN cc_start: 0.6521 (mm110) cc_final: 0.6263 (mm110) REVERT: F 14 LEU cc_start: 0.7875 (tt) cc_final: 0.7469 (mp) REVERT: F 45 LYS cc_start: 0.7014 (mmtt) cc_final: 0.6186 (mtpp) REVERT: F 100 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.5768 (ptp-170) outliers start: 38 outliers final: 27 residues processed: 209 average time/residue: 0.5048 time to fit residues: 155.6245 Evaluate side-chains 206 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain D residue 648 ASN Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 34 TYR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 105 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 57 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.179600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.138746 restraints weight = 36344.004| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.63 r_work: 0.3719 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12672 Z= 0.143 Angle : 0.547 4.384 17196 Z= 0.294 Chirality : 0.045 0.165 1930 Planarity : 0.005 0.046 2196 Dihedral : 4.545 21.235 1686 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.67 % Allowed : 9.87 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.46 (0.21), residues: 1542 helix: 1.63 (0.41), residues: 166 sheet: -0.37 (0.21), residues: 580 loop : -0.59 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 658 HIS 0.004 0.001 HIS A 471 PHE 0.011 0.001 PHE A 629 TYR 0.014 0.002 TYR B 86 ARG 0.002 0.000 ARG D 427 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 466) hydrogen bonds : angle 5.92425 ( 1230) covalent geometry : bond 0.00340 (12672) covalent geometry : angle 0.54736 (17196) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.7146 (mt0) cc_final: 0.6841 (mt0) REVERT: A 239 MET cc_start: 0.7185 (mmp) cc_final: 0.6943 (mmm) REVERT: A 572 LYS cc_start: 0.7692 (pttt) cc_final: 0.7210 (pptt) REVERT: A 574 LYS cc_start: 0.7454 (ptpt) cc_final: 0.6823 (ttpp) REVERT: A 648 ASN cc_start: 0.7770 (OUTLIER) cc_final: 0.7521 (m110) REVERT: C 14 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7493 (mp) REVERT: C 45 LYS cc_start: 0.7130 (mmtt) cc_final: 0.6245 (mtpp) REVERT: C 100 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.5717 (ptp-170) REVERT: D 167 GLU cc_start: 0.7080 (tt0) cc_final: 0.6878 (tm-30) REVERT: D 178 GLN cc_start: 0.7166 (mt0) cc_final: 0.6863 (mt0) REVERT: D 239 MET cc_start: 0.7194 (mmp) cc_final: 0.6951 (mmm) REVERT: D 648 ASN cc_start: 0.7794 (OUTLIER) cc_final: 0.7551 (m110) REVERT: E 79 GLN cc_start: 0.6554 (mm110) cc_final: 0.6286 (mm110) REVERT: F 14 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7475 (mp) REVERT: F 45 LYS cc_start: 0.7123 (mmtt) cc_final: 0.6233 (mtpp) REVERT: F 100 ARG cc_start: 0.6850 (OUTLIER) cc_final: 0.5740 (ptp-170) outliers start: 37 outliers final: 25 residues processed: 207 average time/residue: 0.4825 time to fit residues: 147.7372 Evaluate side-chains 213 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain D residue 648 ASN Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 34 TYR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 118 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN D 196 ASN F 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.177091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.136495 restraints weight = 36717.123| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.61 r_work: 0.3676 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12672 Z= 0.200 Angle : 0.597 4.834 17196 Z= 0.322 Chirality : 0.046 0.167 1930 Planarity : 0.006 0.047 2196 Dihedral : 4.810 25.121 1686 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.88 % Allowed : 10.81 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.89 (0.21), residues: 1542 helix: 0.83 (0.40), residues: 178 sheet: -0.51 (0.21), residues: 578 loop : -0.91 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 466 HIS 0.003 0.001 HIS A 595 PHE 0.014 0.002 PHE A 629 TYR 0.020 0.002 TYR C 33 ARG 0.004 0.001 ARG A 427 Details of bonding type rmsd hydrogen bonds : bond 0.04256 ( 466) hydrogen bonds : angle 6.02945 ( 1230) covalent geometry : bond 0.00479 (12672) covalent geometry : angle 0.59728 (17196) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.4755 (mtp) cc_final: 0.2620 (tpt) REVERT: A 178 GLN cc_start: 0.7165 (mt0) cc_final: 0.6931 (mt0) REVERT: A 239 MET cc_start: 0.7237 (mmp) cc_final: 0.7016 (mmm) REVERT: A 572 LYS cc_start: 0.7714 (pttt) cc_final: 0.7201 (pptt) REVERT: A 648 ASN cc_start: 0.7724 (OUTLIER) cc_final: 0.7368 (m110) REVERT: C 14 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7512 (mp) REVERT: C 45 LYS cc_start: 0.7115 (mmtt) cc_final: 0.6222 (mtpp) REVERT: C 100 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.4913 (ptp-170) REVERT: D 178 GLN cc_start: 0.7195 (mt0) cc_final: 0.6961 (mt0) REVERT: D 239 MET cc_start: 0.7235 (mmp) cc_final: 0.7018 (mmm) REVERT: D 648 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7347 (m110) REVERT: F 14 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7504 (mp) REVERT: F 45 LYS cc_start: 0.7116 (mmtt) cc_final: 0.6224 (mtpp) REVERT: F 100 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.4952 (ptp-170) outliers start: 40 outliers final: 27 residues processed: 218 average time/residue: 0.5466 time to fit residues: 178.5997 Evaluate side-chains 221 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain D residue 648 ASN Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 34 TYR Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 154 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN D 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.177113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.136634 restraints weight = 36779.177| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.61 r_work: 0.3671 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.5723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12672 Z= 0.179 Angle : 0.585 4.761 17196 Z= 0.314 Chirality : 0.046 0.168 1930 Planarity : 0.006 0.049 2196 Dihedral : 4.783 21.743 1686 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.67 % Allowed : 11.10 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.83 (0.21), residues: 1542 helix: 0.92 (0.40), residues: 178 sheet: -0.51 (0.21), residues: 574 loop : -0.86 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 35 HIS 0.003 0.001 HIS D 245 PHE 0.013 0.002 PHE A 629 TYR 0.017 0.002 TYR C 33 ARG 0.003 0.000 ARG D 427 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 466) hydrogen bonds : angle 5.95741 ( 1230) covalent geometry : bond 0.00426 (12672) covalent geometry : angle 0.58534 (17196) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.7205 (mt0) cc_final: 0.6934 (mt0) REVERT: A 239 MET cc_start: 0.7233 (mmp) cc_final: 0.7024 (mmm) REVERT: A 383 ARG cc_start: 0.6417 (mtm-85) cc_final: 0.6206 (mtm-85) REVERT: A 572 LYS cc_start: 0.7709 (pttt) cc_final: 0.7207 (pptt) REVERT: A 648 ASN cc_start: 0.7725 (OUTLIER) cc_final: 0.7283 (m110) REVERT: C 14 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7557 (mp) REVERT: C 45 LYS cc_start: 0.7111 (mmtt) cc_final: 0.6182 (mtpp) REVERT: C 100 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.4970 (ptp-170) REVERT: D 178 GLN cc_start: 0.7224 (mt0) cc_final: 0.6955 (mt0) REVERT: D 239 MET cc_start: 0.7224 (mmp) cc_final: 0.7016 (mmm) REVERT: D 648 ASN cc_start: 0.7724 (OUTLIER) cc_final: 0.7317 (m110) REVERT: E 79 GLN cc_start: 0.6523 (mm110) cc_final: 0.6267 (mm110) REVERT: F 14 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7548 (mp) REVERT: F 45 LYS cc_start: 0.7152 (mmtt) cc_final: 0.6204 (mtpp) REVERT: F 100 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.5019 (ptp-170) outliers start: 37 outliers final: 29 residues processed: 206 average time/residue: 0.5018 time to fit residues: 152.1784 Evaluate side-chains 217 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain D residue 648 ASN Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 34 TYR Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 126 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 30 optimal weight: 0.0770 chunk 146 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 38 optimal weight: 0.0980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN C 31 ASN D 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.178927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.137844 restraints weight = 36630.915| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.62 r_work: 0.3718 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12672 Z= 0.128 Angle : 0.542 4.979 17196 Z= 0.289 Chirality : 0.045 0.167 1930 Planarity : 0.005 0.045 2196 Dihedral : 4.619 24.452 1686 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.23 % Allowed : 11.74 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.71 (0.21), residues: 1542 helix: 1.21 (0.41), residues: 178 sheet: -0.44 (0.21), residues: 578 loop : -0.82 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 658 HIS 0.003 0.001 HIS A 471 PHE 0.012 0.001 PHE D 629 TYR 0.016 0.001 TYR E 55 ARG 0.003 0.000 ARG E 66 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 466) hydrogen bonds : angle 5.75794 ( 1230) covalent geometry : bond 0.00305 (12672) covalent geometry : angle 0.54231 (17196) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.4770 (mtp) cc_final: 0.2621 (tpt) REVERT: A 178 GLN cc_start: 0.7106 (mt0) cc_final: 0.6847 (mt0) REVERT: A 572 LYS cc_start: 0.7587 (pttt) cc_final: 0.7058 (pptt) REVERT: A 648 ASN cc_start: 0.7690 (OUTLIER) cc_final: 0.7376 (m110) REVERT: C 14 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7560 (mp) REVERT: C 45 LYS cc_start: 0.7126 (mmtt) cc_final: 0.6215 (mtpp) REVERT: C 100 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.4963 (ptp-170) REVERT: D 178 GLN cc_start: 0.7139 (mt0) cc_final: 0.6908 (mt0) REVERT: D 648 ASN cc_start: 0.7636 (OUTLIER) cc_final: 0.7339 (m110) REVERT: E 79 GLN cc_start: 0.6352 (mm110) cc_final: 0.6100 (mm110) REVERT: F 14 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7503 (mp) REVERT: F 45 LYS cc_start: 0.7138 (mmtt) cc_final: 0.6224 (mtpp) outliers start: 31 outliers final: 26 residues processed: 204 average time/residue: 0.5287 time to fit residues: 158.7235 Evaluate side-chains 210 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain D residue 648 ASN Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 34 TYR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 122 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 115 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.0970 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN D 196 ASN D 438 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.177872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.137196 restraints weight = 36612.939| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.61 r_work: 0.3712 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12672 Z= 0.155 Angle : 0.567 7.112 17196 Z= 0.300 Chirality : 0.045 0.167 1930 Planarity : 0.005 0.047 2196 Dihedral : 4.646 21.592 1686 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.67 % Allowed : 11.31 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.81 (0.21), residues: 1542 helix: 1.12 (0.40), residues: 178 sheet: -0.47 (0.21), residues: 578 loop : -0.92 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 658 HIS 0.003 0.001 HIS A 471 PHE 0.012 0.001 PHE D 629 TYR 0.016 0.002 TYR E 86 ARG 0.003 0.000 ARG E 66 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 466) hydrogen bonds : angle 5.76387 ( 1230) covalent geometry : bond 0.00373 (12672) covalent geometry : angle 0.56710 (17196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14065.68 seconds wall clock time: 241 minutes 51.86 seconds (14511.86 seconds total)