Starting phenix.real_space_refine on Mon Aug 25 02:16:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sml_40590/08_2025/8sml_40590_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sml_40590/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8sml_40590/08_2025/8sml_40590_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sml_40590/08_2025/8sml_40590_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sml_40590/08_2025/8sml_40590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sml_40590/08_2025/8sml_40590.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.36, per 1000 atoms: 0.18 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: 1.86 Conformation dependent library (CDL) restraints added in 642.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.71 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: 5.65 Time building geometry restraints manager: 2.74 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: 0.03 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: 12.380 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: 0.150 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.200 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.070 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.012 0.001 ARG D 212 TYR 0.073 0.007 TYR F 56 PHE 0.072 0.003 PHE E 98 TRP 0.065 0.008 TRP C 111 HIS 0.009 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00985 (12672) covalent geometry : angle 1.00802 (17196) hydrogen bonds : bond 0.18060 ( 466) hydrogen bonds : angle 9.17544 ( 1230) *********************** 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 : 0.753 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: 0.2491 time to fit residues: 125.2082 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 : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 569 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.192153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.150708 restraints weight = 34862.447| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.58 r_work: 0.3881 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12672 Z= 0.182 Angle : 0.601 5.002 17196 Z= 0.334 Chirality : 0.046 0.186 1930 Planarity : 0.005 0.045 2196 Dihedral : 4.615 22.933 1686 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.80 % Allowed : 6.77 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.21), residues: 1542 helix: 1.00 (0.38), residues: 168 sheet: 0.12 (0.20), residues: 608 loop : 0.21 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 212 TYR 0.012 0.002 TYR D 250 PHE 0.011 0.001 PHE D 285 TRP 0.011 0.001 TRP F 49 HIS 0.010 0.001 HIS D 471 Details of bonding type rmsd covalent geometry : bond 0.00392 (12672) covalent geometry : angle 0.60125 (17196) hydrogen bonds : bond 0.06775 ( 466) hydrogen bonds : angle 7.40215 ( 1230) *********************** 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 237 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 0.486 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 239 MET cc_start: 0.7078 (mmp) cc_final: 0.6809 (mmm) REVERT: A 509 HIS cc_start: 0.7237 (m-70) cc_final: 0.6989 (m-70) REVERT: A 572 LYS cc_start: 0.7552 (pttt) cc_final: 0.7282 (pttm) REVERT: C 21 LEU cc_start: 0.6983 (tp) cc_final: 0.6653 (tp) REVERT: C 106 TYR cc_start: 0.7236 (t80) cc_final: 0.6971 (t80) REVERT: D 239 MET cc_start: 0.7047 (mmp) cc_final: 0.6781 (mmm) REVERT: D 509 HIS cc_start: 0.7173 (m-70) cc_final: 0.6933 (m-70) REVERT: D 572 LYS cc_start: 0.7478 (pttt) cc_final: 0.7183 (pttm) REVERT: F 21 LEU cc_start: 0.6957 (tp) cc_final: 0.6601 (tp) outliers start: 25 outliers final: 13 residues processed: 229 average time/residue: 0.2406 time to fit residues: 79.7677 Evaluate side-chains 192 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ASP 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 209 ASP 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 103 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 46 optimal weight: 0.4980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 D 438 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.183997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.142813 restraints weight = 35375.761| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.55 r_work: 0.3787 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.4069 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= 0.179 Angle : 0.607 5.049 17196 Z= 0.327 Chirality : 0.046 0.175 1930 Planarity : 0.005 0.048 2196 Dihedral : 4.603 20.733 1686 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.95 % Allowed : 7.93 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.21), residues: 1542 helix: 1.23 (0.39), residues: 166 sheet: -0.22 (0.20), residues: 604 loop : -0.09 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 536 TYR 0.021 0.002 TYR E 49 PHE 0.015 0.002 PHE D 629 TRP 0.012 0.002 TRP F 49 HIS 0.006 0.001 HIS D 471 Details of bonding type rmsd covalent geometry : bond 0.00403 (12672) covalent geometry : angle 0.60735 (17196) hydrogen bonds : bond 0.04980 ( 466) hydrogen bonds : angle 6.59506 ( 1230) *********************** 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 235 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.509 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: 0.7127 (mmp) cc_final: 0.6856 (mmm) REVERT: A 572 LYS cc_start: 0.7718 (pttt) cc_final: 0.7229 (pptt) REVERT: C 69 ARG cc_start: 0.7831 (mtm110) cc_final: 0.7346 (ttp-110) REVERT: D 239 MET cc_start: 0.7121 (mmp) cc_final: 0.6852 (mmm) REVERT: D 589 MET cc_start: 0.7040 (ptt) cc_final: 0.6802 (ptt) outliers start: 27 outliers final: 16 residues processed: 225 average time/residue: 0.2426 time to fit residues: 77.8831 Evaluate side-chains 202 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 LEU 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 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 438 ASN 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 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 113 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 119 optimal weight: 0.4980 chunk 141 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.183755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.142397 restraints weight = 35682.871| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.50 r_work: 0.3775 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12672 Z= 0.149 Angle : 0.558 4.472 17196 Z= 0.300 Chirality : 0.045 0.169 1930 Planarity : 0.005 0.047 2196 Dihedral : 4.499 21.861 1686 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.95 % Allowed : 9.37 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.20), residues: 1542 helix: 1.55 (0.40), residues: 166 sheet: -0.32 (0.21), residues: 576 loop : -0.19 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 100 TYR 0.017 0.002 TYR B 49 PHE 0.012 0.001 PHE D 629 TRP 0.009 0.001 TRP F 49 HIS 0.003 0.001 HIS D 595 Details of bonding type rmsd covalent geometry : bond 0.00346 (12672) covalent geometry : angle 0.55783 (17196) hydrogen bonds : bond 0.04518 ( 466) hydrogen bonds : angle 6.21096 ( 1230) *********************** 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 222 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.379 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: 0.7085 (mmp) cc_final: 0.6813 (mmm) REVERT: A 329 LYS cc_start: 0.7623 (mttm) cc_final: 0.7174 (mmmt) REVERT: A 572 LYS cc_start: 0.7679 (pttt) cc_final: 0.7190 (pptt) REVERT: A 648 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7558 (m110) REVERT: B 66 ARG cc_start: 0.7864 (ttt-90) cc_final: 0.7588 (ttt-90) REVERT: D 239 MET cc_start: 0.7125 (mmp) cc_final: 0.6853 (mmm) REVERT: D 329 LYS cc_start: 0.7569 (mttm) cc_final: 0.7115 (mmmt) REVERT: D 589 MET cc_start: 0.7173 (ptt) cc_final: 0.6596 (ptt) REVERT: D 648 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7552 (m110) REVERT: E 66 ARG cc_start: 0.7886 (ttt-90) cc_final: 0.7623 (ttt-90) outliers start: 27 outliers final: 18 residues processed: 213 average time/residue: 0.2199 time to fit residues: 67.9633 Evaluate side-chains 205 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 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 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 123 THR Chi-restraints excluded: chain D residue 118 CYS 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 D residue 648 ASN Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 196 ASN D 26 GLN D 196 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.177542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.136228 restraints weight = 36685.323| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.70 r_work: 0.3687 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.5019 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= 0.213 Angle : 0.618 5.077 17196 Z= 0.334 Chirality : 0.047 0.167 1930 Planarity : 0.006 0.050 2196 Dihedral : 4.817 20.581 1686 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.95 % Allowed : 8.86 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.20), residues: 1542 helix: 1.29 (0.41), residues: 166 sheet: -0.57 (0.21), residues: 572 loop : -0.67 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 427 TYR 0.021 0.003 TYR B 49 PHE 0.016 0.002 PHE E 98 TRP 0.014 0.002 TRP D 466 HIS 0.004 0.001 HIS D 595 Details of bonding type rmsd covalent geometry : bond 0.00505 (12672) covalent geometry : angle 0.61840 (17196) hydrogen bonds : bond 0.04629 ( 466) hydrogen bonds : angle 6.19288 ( 1230) *********************** 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 234 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 0.910 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: 0.7224 (tt0) cc_final: 0.6988 (tm-30) REVERT: A 239 MET cc_start: 0.7174 (mmp) cc_final: 0.6930 (mmm) REVERT: A 476 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7564 (pt) REVERT: A 572 LYS cc_start: 0.7713 (pttt) cc_final: 0.7183 (pptt) REVERT: A 648 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7379 (m110) REVERT: C 14 LEU cc_start: 0.7869 (tt) cc_final: 0.7490 (mp) REVERT: C 45 LYS cc_start: 0.6966 (mmtt) cc_final: 0.6187 (mttm) REVERT: C 100 ARG cc_start: 0.6791 (OUTLIER) cc_final: 0.5769 (ptp-170) REVERT: D 80 MET cc_start: 0.5009 (mtp) cc_final: 0.2904 (tpt) REVERT: D 167 GLU cc_start: 0.7210 (tt0) cc_final: 0.6998 (tm-30) REVERT: D 239 MET cc_start: 0.7171 (mmp) cc_final: 0.6930 (mmm) REVERT: D 476 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7617 (pt) REVERT: D 589 MET cc_start: 0.7096 (ptt) cc_final: 0.6671 (ptt) REVERT: D 648 ASN cc_start: 0.7794 (OUTLIER) cc_final: 0.7403 (m110) REVERT: F 14 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7487 (mp) REVERT: F 45 LYS cc_start: 0.6975 (mmtt) cc_final: 0.6190 (mttm) REVERT: F 100 ARG cc_start: 0.6821 (OUTLIER) cc_final: 0.5865 (ptp-170) outliers start: 41 outliers final: 28 residues processed: 218 average time/residue: 0.2306 time to fit residues: 72.8926 Evaluate side-chains 213 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 476 LEU 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 100 ARG Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 217 THR 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 464 SER Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 540 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 19 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 53 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 41 optimal weight: 0.1980 chunk 61 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4285 r_free = 0.4285 target = 0.178671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.137246 restraints weight = 36189.935| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.70 r_work: 0.3706 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.5200 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= 0.145 Angle : 0.550 4.225 17196 Z= 0.295 Chirality : 0.045 0.165 1930 Planarity : 0.005 0.047 2196 Dihedral : 4.610 23.662 1686 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.23 % Allowed : 10.01 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.21), residues: 1542 helix: 1.52 (0.41), residues: 166 sheet: -0.42 (0.21), residues: 582 loop : -0.59 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 427 TYR 0.014 0.002 TYR B 49 PHE 0.012 0.001 PHE D 629 TRP 0.011 0.001 TRP D 658 HIS 0.003 0.001 HIS A 595 Details of bonding type rmsd covalent geometry : bond 0.00340 (12672) covalent geometry : angle 0.55046 (17196) hydrogen bonds : bond 0.04126 ( 466) hydrogen bonds : angle 5.96617 ( 1230) *********************** 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 223 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.561 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: 0.7110 (tt0) cc_final: 0.6875 (tm-30) REVERT: A 239 MET cc_start: 0.7169 (mmp) cc_final: 0.6930 (mmm) REVERT: A 572 LYS cc_start: 0.7654 (pttt) cc_final: 0.7152 (pptt) REVERT: A 648 ASN cc_start: 0.7688 (OUTLIER) cc_final: 0.7429 (m110) REVERT: C 14 LEU cc_start: 0.7855 (tt) cc_final: 0.7434 (mp) REVERT: C 45 LYS cc_start: 0.7007 (mmtt) cc_final: 0.6166 (mtpp) REVERT: D 80 MET cc_start: 0.4920 (mtp) cc_final: 0.2873 (tpt) REVERT: D 167 GLU cc_start: 0.7098 (tt0) cc_final: 0.6869 (tm-30) REVERT: D 180 MET cc_start: 0.7458 (mtt) cc_final: 0.7179 (mtt) REVERT: D 239 MET cc_start: 0.7165 (mmp) cc_final: 0.6931 (mmm) REVERT: D 648 ASN cc_start: 0.7720 (OUTLIER) cc_final: 0.7455 (m110) REVERT: E 79 GLN cc_start: 0.6463 (mm110) cc_final: 0.6201 (mm110) REVERT: F 14 LEU cc_start: 0.7857 (tt) cc_final: 0.7470 (mp) REVERT: F 45 LYS cc_start: 0.7002 (mmtt) cc_final: 0.6166 (mtpp) outliers start: 31 outliers final: 24 residues processed: 210 average time/residue: 0.2203 time to fit residues: 69.1817 Evaluate side-chains 206 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 413 SER Chi-restraints excluded: chain A residue 438 ASN 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 15 VAL Chi-restraints excluded: chain C residue 34 TYR 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 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 F residue 15 VAL Chi-restraints excluded: chain F residue 34 TYR 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 127 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 80 optimal weight: 0.3980 chunk 152 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 F 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.177516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.137102 restraints weight = 36651.801| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.61 r_work: 0.3697 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.5444 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= 0.181 Angle : 0.577 4.772 17196 Z= 0.309 Chirality : 0.046 0.164 1930 Planarity : 0.006 0.049 2196 Dihedral : 4.700 20.689 1686 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.03 % Allowed : 10.45 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.21), residues: 1542 helix: 1.38 (0.41), residues: 166 sheet: -0.55 (0.21), residues: 584 loop : -0.81 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 427 TYR 0.019 0.002 TYR B 86 PHE 0.013 0.002 PHE A 629 TRP 0.011 0.002 TRP D 658 HIS 0.003 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00433 (12672) covalent geometry : angle 0.57654 (17196) hydrogen bonds : bond 0.04238 ( 466) hydrogen bonds : angle 5.98430 ( 1230) *********************** 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 229 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 0.641 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: A 167 GLU cc_start: 0.7027 (tt0) cc_final: 0.6809 (tm-30) REVERT: A 239 MET cc_start: 0.7197 (mmp) cc_final: 0.6972 (mmm) REVERT: A 572 LYS cc_start: 0.7744 (pttt) cc_final: 0.7240 (pptt) REVERT: A 648 ASN cc_start: 0.7741 (OUTLIER) cc_final: 0.7457 (m110) REVERT: C 14 LEU cc_start: 0.7867 (tt) cc_final: 0.7458 (mp) REVERT: C 45 LYS cc_start: 0.7101 (mmtt) cc_final: 0.6211 (mtpp) REVERT: D 80 MET cc_start: 0.4953 (mtp) cc_final: 0.2854 (tpt) REVERT: D 167 GLU cc_start: 0.7043 (tt0) cc_final: 0.6822 (tm-30) REVERT: D 239 MET cc_start: 0.7219 (mmp) cc_final: 0.6997 (mmm) REVERT: D 648 ASN cc_start: 0.7770 (OUTLIER) cc_final: 0.7482 (m110) REVERT: F 14 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7495 (mp) REVERT: F 45 LYS cc_start: 0.7109 (mmtt) cc_final: 0.6219 (mtpp) outliers start: 42 outliers final: 28 residues processed: 210 average time/residue: 0.1947 time to fit residues: 61.8829 Evaluate side-chains 216 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 325 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 438 ASN 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 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 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 392 VAL Chi-restraints excluded: chain D residue 413 SER 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 75 ASP 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 52 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 156 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4274 r_free = 0.4274 target = 0.177943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.137333 restraints weight = 36562.406| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.61 r_work: 0.3692 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12672 Z= 0.158 Angle : 0.557 4.698 17196 Z= 0.298 Chirality : 0.045 0.168 1930 Planarity : 0.005 0.047 2196 Dihedral : 4.675 24.217 1686 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.88 % Allowed : 10.95 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.21), residues: 1542 helix: 1.54 (0.41), residues: 166 sheet: -0.54 (0.21), residues: 582 loop : -0.82 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 427 TYR 0.014 0.002 TYR B 49 PHE 0.011 0.001 PHE A 629 TRP 0.012 0.002 TRP D 658 HIS 0.003 0.001 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00379 (12672) covalent geometry : angle 0.55723 (17196) hydrogen bonds : bond 0.04011 ( 466) hydrogen bonds : angle 5.85751 ( 1230) *********************** 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 233 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 0.667 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 80 MET cc_start: 0.4758 (mtp) cc_final: 0.2648 (tpt) REVERT: A 167 GLU cc_start: 0.7029 (tt0) cc_final: 0.6780 (tm-30) REVERT: A 239 MET cc_start: 0.7231 (mmp) cc_final: 0.7016 (mmm) REVERT: A 254 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7300 (mp) REVERT: A 572 LYS cc_start: 0.7718 (pttt) cc_final: 0.7200 (pptt) REVERT: A 648 ASN cc_start: 0.7669 (OUTLIER) cc_final: 0.7400 (m110) REVERT: C 14 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7486 (mp) REVERT: C 45 LYS cc_start: 0.7118 (mmtt) cc_final: 0.6240 (mtpp) REVERT: C 100 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.4927 (ptp-170) REVERT: D 80 MET cc_start: 0.4909 (mtp) cc_final: 0.2848 (tpt) REVERT: D 167 GLU cc_start: 0.7044 (tt0) cc_final: 0.6822 (tm-30) REVERT: D 239 MET cc_start: 0.7229 (mmp) cc_final: 0.7018 (mmm) REVERT: D 648 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7418 (m110) REVERT: E 79 GLN cc_start: 0.6514 (mm110) cc_final: 0.6236 (mm110) REVERT: F 14 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7483 (mp) REVERT: F 45 LYS cc_start: 0.7136 (mmtt) cc_final: 0.6263 (mtpp) REVERT: F 100 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.5714 (ptp-170) outliers start: 40 outliers final: 27 residues processed: 216 average time/residue: 0.2113 time to fit residues: 68.0421 Evaluate side-chains 219 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 348 MET 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 153 ASN Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 325 THR 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 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 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 94 optimal weight: 0.9990 chunk 157 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 117 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 156 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.177591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.137059 restraints weight = 36771.984| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.61 r_work: 0.3681 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12672 Z= 0.160 Angle : 0.564 4.960 17196 Z= 0.300 Chirality : 0.045 0.168 1930 Planarity : 0.005 0.049 2196 Dihedral : 4.681 20.799 1686 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.03 % Allowed : 11.38 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.21), residues: 1542 helix: 1.06 (0.41), residues: 178 sheet: -0.51 (0.21), residues: 582 loop : -0.97 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 427 TYR 0.014 0.002 TYR B 86 PHE 0.013 0.001 PHE D 629 TRP 0.012 0.002 TRP D 658 HIS 0.002 0.001 HIS A 595 Details of bonding type rmsd covalent geometry : bond 0.00384 (12672) covalent geometry : angle 0.56416 (17196) hydrogen bonds : bond 0.04018 ( 466) hydrogen bonds : angle 5.83568 ( 1230) *********************** 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 231 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 0.762 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: A 167 GLU cc_start: 0.7052 (tt0) cc_final: 0.6803 (tm-30) REVERT: A 239 MET cc_start: 0.7262 (mmp) cc_final: 0.7047 (mmm) REVERT: A 254 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7390 (mp) REVERT: A 383 ARG cc_start: 0.6348 (mtm-85) cc_final: 0.6145 (mtm-85) REVERT: A 572 LYS cc_start: 0.7699 (pttt) cc_final: 0.7175 (pptt) REVERT: A 648 ASN cc_start: 0.7699 (OUTLIER) cc_final: 0.7311 (m110) REVERT: B 4 MET cc_start: 0.6635 (ttt) cc_final: 0.6353 (ttt) REVERT: C 14 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7496 (mp) REVERT: C 45 LYS cc_start: 0.7155 (mmtt) cc_final: 0.6252 (mtpp) REVERT: D 80 MET cc_start: 0.4936 (mtp) cc_final: 0.2748 (tpt) REVERT: D 167 GLU cc_start: 0.7063 (tt0) cc_final: 0.6818 (tm-30) REVERT: D 239 MET cc_start: 0.7256 (mmp) cc_final: 0.7046 (mmm) REVERT: D 383 ARG cc_start: 0.6346 (mtm-85) cc_final: 0.6144 (mtm-85) REVERT: D 648 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7308 (m110) REVERT: E 79 GLN cc_start: 0.6593 (mm110) cc_final: 0.6314 (mm110) REVERT: F 14 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7495 (mp) REVERT: F 45 LYS cc_start: 0.7118 (mmtt) cc_final: 0.6181 (mtpp) outliers start: 42 outliers final: 35 residues processed: 212 average time/residue: 0.1871 time to fit residues: 58.8839 Evaluate side-chains 225 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 438 ASN 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 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 325 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 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 127 optimal weight: 0.0980 chunk 114 optimal weight: 0.7980 chunk 54 optimal weight: 0.0970 chunk 123 optimal weight: 0.0670 chunk 118 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 196 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 = 0.4290 r_free = 0.4290 target = 0.179132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.138442 restraints weight = 35976.984| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.66 r_work: 0.3701 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.5752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12672 Z= 0.103 Angle : 0.516 5.085 17196 Z= 0.272 Chirality : 0.044 0.167 1930 Planarity : 0.005 0.046 2196 Dihedral : 4.428 23.111 1686 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.66 % Allowed : 12.61 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.21), residues: 1542 helix: 1.41 (0.41), residues: 178 sheet: -0.30 (0.21), residues: 606 loop : -0.78 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 66 TYR 0.011 0.001 TYR B 49 PHE 0.008 0.001 PHE A 629 TRP 0.014 0.001 TRP D 658 HIS 0.003 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00243 (12672) covalent geometry : angle 0.51594 (17196) hydrogen bonds : bond 0.03614 ( 466) hydrogen bonds : angle 5.57545 ( 1230) ********************** 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 213 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.698 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 80 MET cc_start: 0.4614 (mtp) cc_final: 0.2444 (tpt) REVERT: A 167 GLU cc_start: 0.6986 (tt0) cc_final: 0.6720 (tm-30) REVERT: A 239 MET cc_start: 0.7214 (mmp) cc_final: 0.6995 (mmm) REVERT: A 572 LYS cc_start: 0.7603 (pttt) cc_final: 0.7060 (pptt) REVERT: A 648 ASN cc_start: 0.7597 (OUTLIER) cc_final: 0.7309 (m110) REVERT: B 4 MET cc_start: 0.6461 (ttt) cc_final: 0.6186 (ttt) REVERT: C 14 LEU cc_start: 0.7884 (tt) cc_final: 0.7491 (mp) REVERT: C 45 LYS cc_start: 0.7077 (mmtt) cc_final: 0.6146 (mtpp) REVERT: C 100 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.5463 (ptp-170) REVERT: D 80 MET cc_start: 0.4868 (mtp) cc_final: 0.2616 (tpt) REVERT: D 167 GLU cc_start: 0.7037 (tt0) cc_final: 0.6773 (tm-30) REVERT: D 239 MET cc_start: 0.7207 (mmp) cc_final: 0.6995 (mmm) REVERT: D 648 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7326 (m110) REVERT: E 79 GLN cc_start: 0.6182 (mm110) cc_final: 0.5895 (mm110) REVERT: F 14 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7507 (mp) REVERT: F 45 LYS cc_start: 0.7119 (mmtt) cc_final: 0.6168 (mtpp) REVERT: F 100 ARG cc_start: 0.6645 (OUTLIER) cc_final: 0.5524 (ptp-170) outliers start: 23 outliers final: 15 residues processed: 205 average time/residue: 0.2046 time to fit residues: 61.9533 Evaluate side-chains 204 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 476 LEU 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 34 TYR Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 476 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 3 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 140 optimal weight: 0.0970 chunk 47 optimal weight: 0.1980 chunk 83 optimal weight: 0.5980 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 = 0.4302 r_free = 0.4302 target = 0.180592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.139559 restraints weight = 36296.230| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.62 r_work: 0.3742 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.5811 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= 0.112 Angle : 0.518 7.036 17196 Z= 0.272 Chirality : 0.044 0.166 1930 Planarity : 0.005 0.046 2196 Dihedral : 4.350 19.541 1686 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.80 % Allowed : 12.97 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.21), residues: 1542 helix: 1.40 (0.41), residues: 178 sheet: -0.23 (0.21), residues: 608 loop : -0.76 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 66 TYR 0.015 0.001 TYR E 55 PHE 0.010 0.001 PHE D 261 TRP 0.012 0.001 TRP D 658 HIS 0.002 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00268 (12672) covalent geometry : angle 0.51770 (17196) hydrogen bonds : bond 0.03598 ( 466) hydrogen bonds : angle 5.50980 ( 1230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6517.22 seconds wall clock time: 111 minutes 2.88 seconds (6662.88 seconds total)