Starting phenix.real_space_refine on Mon Sep 30 06:13:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sml_40590/09_2024/8sml_40590_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sml_40590/09_2024/8sml_40590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sml_40590/09_2024/8sml_40590.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sml_40590/09_2024/8sml_40590.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sml_40590/09_2024/8sml_40590_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sml_40590/09_2024/8sml_40590_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.441 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 S 78 5.16 5 C 7894 2.51 5 N 2068 2.21 5 O 2348 1.98 5 H 12234 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24628 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 8910 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 39, 'TRANS': 530} Chain breaks: 10 Chain: "B" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1573 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1828 Classifications: {'peptide': 121} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 8910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 8910 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 39, 'TRANS': 530} Chain breaks: 10 Chain: "E" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1573 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1828 Classifications: {'peptide': 121} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 14.02, per 1000 atoms: 0.57 Number of scatterers: 24628 At special positions: 0 Unit cell: (156.145, 122.745, 68.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 78 16.00 O 2348 8.00 N 2068 7.00 C 7894 6.00 H 12234 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.94 Conformation dependent library (CDL) restraints added in 2.2 seconds 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2964 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 34 sheets defined 16.7% alpha, 36.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'A' and resid 164 through 168 removed outlier: 3.757A pdb=" N ASP A 168 " --> pdb=" O ASP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'A' and resid 317 through 330 Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 444 through 453 Processing helix chain 'A' and resid 454 through 458 Processing helix chain 'A' and resid 471 through 474 Processing helix chain 'A' and resid 494 through 507 Processing helix chain 'A' and resid 527 through 531 Processing helix chain 'A' and resid 532 through 558 removed outlier: 3.974A pdb=" N ASN A 549 " --> pdb=" O CYS A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 562 No H-bonds generated for 'chain 'A' and resid 560 through 562' Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 610 through 621 Processing helix chain 'A' and resid 622 through 624 No H-bonds generated for 'chain 'A' and resid 622 through 624' Processing helix chain 'A' and resid 657 through 661 Processing helix chain 'C' and resid 64 through 67 removed outlier: 3.628A pdb=" N LYS C 67 " --> pdb=" O ASP C 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 64 through 67' Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.757A pdb=" N ASP D 168 " --> pdb=" O ASP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 205 through 208 Processing helix chain 'D' and resid 317 through 330 Processing helix chain 'D' and resid 406 through 408 No H-bonds generated for 'chain 'D' and resid 406 through 408' Processing helix chain 'D' and resid 444 through 453 Processing helix chain 'D' and resid 454 through 458 Processing helix chain 'D' and resid 471 through 474 Processing helix chain 'D' and resid 494 through 507 Processing helix chain 'D' and resid 527 through 531 Processing helix chain 'D' and resid 532 through 558 removed outlier: 3.974A pdb=" N ASN D 549 " --> pdb=" O CYS D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 562 No H-bonds generated for 'chain 'D' and resid 560 through 562' Processing helix chain 'D' and resid 575 through 577 No H-bonds generated for 'chain 'D' and resid 575 through 577' Processing helix chain 'D' and resid 610 through 621 Processing helix chain 'D' and resid 622 through 624 No H-bonds generated for 'chain 'D' and resid 622 through 624' Processing helix chain 'D' and resid 657 through 661 Processing helix chain 'F' and resid 64 through 67 removed outlier: 3.627A pdb=" N LYS F 67 " --> pdb=" O ASP F 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 64 through 67' Processing helix chain 'F' and resid 89 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 removed outlier: 6.854A pdb=" N ILE A 7 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 20 removed outlier: 3.983A pdb=" N VAL A 104 " --> pdb=" O TYR A 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 20 removed outlier: 4.805A pdb=" N ASP A 248 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 213 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 148 through 150 removed outlier: 6.521A pdb=" N ALA A 148 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL A 283 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASP A 273 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU A 199 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 297 through 298 removed outlier: 8.084A pdb=" N VAL A 392 " --> pdb=" O PRO A 365 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL A 367 " --> pdb=" O VAL A 392 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 333 through 336 removed outlier: 6.385A pdb=" N GLN A 306 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR A 335 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL A 308 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG A 650 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL A 308 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN A 648 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 412 removed outlier: 6.325A pdb=" N ILE A 428 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU A 462 " --> pdb=" O ILE A 428 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE A 430 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 416 through 418 Processing sheet with id=AA9, first strand: chain 'A' and resid 476 through 480 removed outlier: 8.123A pdb=" N ILE A 565 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU A 489 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE A 567 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU A 491 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 571 through 573 Processing sheet with id=AB2, first strand: chain 'A' and resid 590 through 592 Processing sheet with id=AB3, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AB4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.542A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SER B 53 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.138A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 6 through 10 Processing sheet with id=AB7, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.189A pdb=" N GLY C 13 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE C 36 " --> pdb=" O SER C 52 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER C 52 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP C 38 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.189A pdb=" N GLY C 13 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 6 through 8 removed outlier: 6.854A pdb=" N ILE D 7 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 15 through 20 removed outlier: 3.983A pdb=" N VAL D 104 " --> pdb=" O TYR D 96 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 15 through 20 removed outlier: 4.804A pdb=" N ASP D 248 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL D 213 " --> pdb=" O VAL D 228 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 148 through 150 removed outlier: 6.521A pdb=" N ALA D 148 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL D 283 " --> pdb=" O ASP D 273 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASP D 273 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU D 199 " --> pdb=" O LEU D 238 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 297 through 298 removed outlier: 8.084A pdb=" N VAL D 392 " --> pdb=" O PRO D 365 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL D 367 " --> pdb=" O VAL D 392 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 333 through 336 removed outlier: 6.385A pdb=" N GLN D 306 " --> pdb=" O LYS D 333 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR D 335 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL D 308 " --> pdb=" O THR D 335 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG D 650 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL D 308 " --> pdb=" O ASN D 648 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN D 648 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 410 through 412 removed outlier: 6.326A pdb=" N ILE D 428 " --> pdb=" O VAL D 460 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU D 462 " --> pdb=" O ILE D 428 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE D 430 " --> pdb=" O LEU D 462 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 416 through 418 Processing sheet with id=AC8, first strand: chain 'D' and resid 476 through 480 removed outlier: 8.123A pdb=" N ILE D 565 " --> pdb=" O PHE D 487 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU D 489 " --> pdb=" O ILE D 565 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE D 567 " --> pdb=" O LEU D 489 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU D 491 " --> pdb=" O ILE D 567 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 571 through 573 Processing sheet with id=AD1, first strand: chain 'D' and resid 590 through 592 Processing sheet with id=AD2, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AD3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.542A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER E 53 " --> pdb=" O TYR E 49 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.139A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 6 through 10 Processing sheet with id=AD6, first strand: chain 'F' and resid 13 through 14 removed outlier: 6.188A pdb=" N GLY F 13 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE F 36 " --> pdb=" O SER F 52 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER F 52 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP F 38 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 13 through 14 removed outlier: 6.188A pdb=" N GLY F 13 " --> pdb=" O THR F 123 " (cutoff:3.500A) 494 hydrogen bonds defined for protein. 1230 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.82 Time building geometry restraints manager: 7.22 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: 0.00 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: 46.600 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 52.950 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.830 ------------------------------------------------------------------------------- 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= 0.635 Angle : 1.008 8.041 17196 Z= 0.650 Chirality : 0.064 0.348 1930 Planarity : 0.007 0.063 2196 Dihedral : 11.401 89.769 4608 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.08 % Favored : 97.80 % Rotamer: Outliers : 0.14 % Allowed : 1.30 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.21), residues: 1542 helix: 0.12 (0.35), residues: 164 sheet: 0.42 (0.21), residues: 584 loop : 0.48 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.008 TRP C 111 HIS 0.009 0.001 HIS C 37 PHE 0.072 0.003 PHE E 98 TYR 0.073 0.007 TYR F 56 ARG 0.012 0.001 ARG D 212 *********************** 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 fitting. rotamer outliers: 2 poor density : 349 time to evaluate : 1.716 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: 0.5328 time to fit residues: 266.4787 Evaluate side-chains 192 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12672 Z= 0.278 Angle : 0.620 4.996 17196 Z= 0.339 Chirality : 0.047 0.188 1930 Planarity : 0.005 0.045 2196 Dihedral : 4.667 23.641 1686 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.66 % Allowed : 6.63 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.21), residues: 1542 helix: 0.90 (0.38), residues: 168 sheet: 0.05 (0.20), residues: 608 loop : 0.12 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 49 HIS 0.010 0.001 HIS D 471 PHE 0.015 0.002 PHE D 285 TYR 0.012 0.002 TYR B 49 ARG 0.003 0.001 ARG D 495 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 212 time to evaluate : 1.866 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: 0.7254 (mmp) cc_final: 0.6996 (mmm) REVERT: A 572 LYS cc_start: 0.7730 (pttt) cc_final: 0.7454 (pttm) REVERT: C 21 LEU cc_start: 0.6824 (tp) cc_final: 0.6555 (tp) REVERT: D 239 MET cc_start: 0.7223 (mmp) cc_final: 0.6954 (mmm) REVERT: D 572 LYS cc_start: 0.7715 (pttt) cc_final: 0.7421 (pttm) REVERT: F 21 LEU cc_start: 0.6901 (tp) cc_final: 0.6612 (tp) outliers start: 23 outliers final: 11 residues processed: 227 average time/residue: 0.5771 time to fit residues: 190.9210 Evaluate side-chains 187 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 176 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain E residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 97 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 245 HIS A 438 ASN A 509 HIS D 215 GLN D 245 HIS D 509 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.4093 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= 0.286 Angle : 0.615 5.074 17196 Z= 0.333 Chirality : 0.046 0.175 1930 Planarity : 0.005 0.049 2196 Dihedral : 4.654 20.924 1686 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.95 % Allowed : 8.36 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.21), residues: 1542 helix: 1.25 (0.40), residues: 166 sheet: -0.29 (0.20), residues: 604 loop : -0.14 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 49 HIS 0.005 0.001 HIS D 471 PHE 0.017 0.002 PHE B 98 TYR 0.022 0.002 TYR E 49 ARG 0.004 0.001 ARG D 495 *********************** 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 233 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 206 time to evaluate : 1.849 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: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.7290 (mmp) cc_final: 0.7047 (mmm) REVERT: A 329 LYS cc_start: 0.7780 (mttt) cc_final: 0.7340 (tptp) REVERT: A 589 MET cc_start: 0.7230 (ptt) cc_final: 0.6981 (ptt) REVERT: C 69 ARG cc_start: 0.7915 (mtm110) cc_final: 0.7568 (ttp-110) REVERT: D 239 MET cc_start: 0.7278 (mmp) cc_final: 0.7032 (mmm) REVERT: D 329 LYS cc_start: 0.7744 (mttt) cc_final: 0.7362 (mmtt) REVERT: D 589 MET cc_start: 0.7237 (ptt) cc_final: 0.6993 (ptt) outliers start: 27 outliers final: 18 residues processed: 223 average time/residue: 0.5350 time to fit residues: 171.0717 Evaluate side-chains 211 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 193 time to evaluate : 1.893 ------------------------------------------------------------------------------- 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 438 ASN Chi-restraints excluded: chain A residue 461 LYS 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 334 LEU Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 461 LYS 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 142 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 41 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN D 196 ASN D 438 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12672 Z= 0.252 Angle : 0.571 4.525 17196 Z= 0.308 Chirality : 0.045 0.171 1930 Planarity : 0.005 0.049 2196 Dihedral : 4.614 23.390 1686 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.02 % Allowed : 9.37 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1542 helix: 1.53 (0.40), residues: 166 sheet: -0.38 (0.20), residues: 602 loop : -0.29 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 466 HIS 0.003 0.001 HIS A 245 PHE 0.013 0.002 PHE D 629 TYR 0.017 0.002 TYR B 49 ARG 0.003 0.000 ARG E 18 *********************** 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 227 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 1.801 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: A 239 MET cc_start: 0.7315 (mmp) cc_final: 0.7071 (mmm) REVERT: A 329 LYS cc_start: 0.7805 (mttt) cc_final: 0.7333 (tptp) REVERT: A 572 LYS cc_start: 0.7828 (pttt) cc_final: 0.7371 (pptt) REVERT: A 589 MET cc_start: 0.7316 (ptt) cc_final: 0.7008 (ptt) REVERT: D 239 MET cc_start: 0.7307 (mmp) cc_final: 0.7060 (mmm) REVERT: D 329 LYS cc_start: 0.7777 (mttt) cc_final: 0.7308 (tptp) REVERT: D 589 MET cc_start: 0.7303 (ptt) cc_final: 0.6851 (ptt) outliers start: 28 outliers final: 19 residues processed: 219 average time/residue: 0.5385 time to fit residues: 169.6271 Evaluate side-chains 205 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 15 VAL 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 410 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 602 PHE Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain E residue 20 THR 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 127 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 113 optimal weight: 0.0970 chunk 63 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 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 196 ASN D 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.4833 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= 0.235 Angle : 0.557 4.265 17196 Z= 0.299 Chirality : 0.045 0.166 1930 Planarity : 0.005 0.078 2196 Dihedral : 4.512 20.067 1686 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.02 % Allowed : 9.08 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.20), residues: 1542 helix: 1.63 (0.41), residues: 166 sheet: -0.44 (0.21), residues: 576 loop : -0.43 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 658 HIS 0.003 0.001 HIS A 595 PHE 0.011 0.001 PHE A 629 TYR 0.014 0.002 TYR E 49 ARG 0.004 0.000 ARG B 66 *********************** 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 223 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 195 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.7355 (mt0) cc_final: 0.7120 (mt0) REVERT: A 239 MET cc_start: 0.7338 (mmp) cc_final: 0.7111 (mmm) REVERT: A 572 LYS cc_start: 0.7845 (pttt) cc_final: 0.7366 (pptt) REVERT: C 45 LYS cc_start: 0.6991 (mmtt) cc_final: 0.6224 (mttm) REVERT: D 178 GLN cc_start: 0.7363 (mt0) cc_final: 0.7136 (mt0) REVERT: D 239 MET cc_start: 0.7307 (mmp) cc_final: 0.7073 (mmm) outliers start: 28 outliers final: 20 residues processed: 211 average time/residue: 0.5189 time to fit residues: 160.5162 Evaluate side-chains 204 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 627 CYS 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 153 ASN Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 627 CYS 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 123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 80 optimal weight: 0.2980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.5172 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= 0.281 Angle : 0.586 4.635 17196 Z= 0.314 Chirality : 0.045 0.166 1930 Planarity : 0.006 0.089 2196 Dihedral : 4.691 24.631 1686 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.59 % Allowed : 9.73 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.20), residues: 1542 helix: 1.34 (0.40), residues: 166 sheet: -0.43 (0.21), residues: 582 loop : -0.68 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 35 HIS 0.003 0.001 HIS A 595 PHE 0.014 0.002 PHE A 629 TYR 0.017 0.002 TYR F 33 ARG 0.008 0.001 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 188 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.7382 (mt0) cc_final: 0.7155 (mt0) REVERT: A 239 MET cc_start: 0.7311 (mmp) cc_final: 0.7087 (mmm) REVERT: A 572 LYS cc_start: 0.7869 (pttt) cc_final: 0.7386 (pptt) REVERT: A 589 MET cc_start: 0.7344 (ptt) cc_final: 0.6944 (ptt) REVERT: C 14 LEU cc_start: 0.8046 (tt) cc_final: 0.7677 (mp) REVERT: C 45 LYS cc_start: 0.7133 (mmtt) cc_final: 0.6329 (mtpp) REVERT: C 100 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.4987 (ptp-170) REVERT: D 178 GLN cc_start: 0.7414 (mt0) cc_final: 0.7129 (mt0) REVERT: D 239 MET cc_start: 0.7302 (mmp) cc_final: 0.7078 (mmm) REVERT: D 476 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7464 (pt) REVERT: F 14 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7652 (mp) REVERT: F 45 LYS cc_start: 0.7140 (mmtt) cc_final: 0.6335 (mtpp) REVERT: F 100 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.5002 (ptp-170) outliers start: 36 outliers final: 27 residues processed: 208 average time/residue: 0.5088 time to fit residues: 156.1729 Evaluate side-chains 207 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 1.794 ------------------------------------------------------------------------------- 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 392 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain B residue 4 MET 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 153 ASN 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 476 LEU Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain E residue 4 MET 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 100 ARG Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 86 optimal weight: 0.0170 chunk 128 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 overall best weight: 0.7418 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.5346 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= 0.252 Angle : 0.563 4.305 17196 Z= 0.302 Chirality : 0.045 0.165 1930 Planarity : 0.005 0.046 2196 Dihedral : 4.616 20.617 1686 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.67 % Allowed : 10.09 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.21), residues: 1542 helix: 1.50 (0.41), residues: 166 sheet: -0.44 (0.21), residues: 582 loop : -0.70 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 658 HIS 0.002 0.001 HIS D 595 PHE 0.012 0.001 PHE A 629 TYR 0.014 0.002 TYR E 49 ARG 0.002 0.000 ARG A 427 *********************** 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 231 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 194 time to evaluate : 1.929 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 80 MET cc_start: 0.4578 (mtp) cc_final: 0.2616 (tpt) REVERT: A 178 GLN cc_start: 0.7422 (mt0) cc_final: 0.7180 (mt0) REVERT: A 239 MET cc_start: 0.7323 (mmp) cc_final: 0.7113 (mmm) REVERT: A 572 LYS cc_start: 0.7870 (pttt) cc_final: 0.7379 (pptt) REVERT: C 14 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7662 (mp) REVERT: C 45 LYS cc_start: 0.7185 (mmtt) cc_final: 0.6320 (mtpp) REVERT: C 100 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.4997 (ptp-170) REVERT: D 178 GLN cc_start: 0.7438 (mt0) cc_final: 0.7162 (mt0) REVERT: D 239 MET cc_start: 0.7314 (mmp) cc_final: 0.7106 (mmm) REVERT: F 14 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7639 (mp) REVERT: F 45 LYS cc_start: 0.7193 (mmtt) cc_final: 0.6330 (mtpp) REVERT: F 100 ARG cc_start: 0.6913 (OUTLIER) cc_final: 0.4986 (ptp-170) outliers start: 37 outliers final: 26 residues processed: 215 average time/residue: 0.4949 time to fit residues: 157.4580 Evaluate side-chains 219 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 189 time to evaluate : 1.864 ------------------------------------------------------------------------------- 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 439 ASP Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 627 CYS 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 50 VAL 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 392 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN D 196 ASN F 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12672 Z= 0.310 Angle : 0.596 4.750 17196 Z= 0.320 Chirality : 0.046 0.170 1930 Planarity : 0.006 0.048 2196 Dihedral : 4.837 25.975 1686 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.24 % Allowed : 10.01 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.21), residues: 1542 helix: 0.84 (0.39), residues: 178 sheet: -0.48 (0.21), residues: 574 loop : -0.91 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 35 HIS 0.003 0.001 HIS D 197 PHE 0.014 0.002 PHE A 629 TYR 0.022 0.002 TYR C 33 ARG 0.004 0.001 ARG D 427 *********************** 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 244 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 199 time to evaluate : 1.879 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 329 LYS cc_start: 0.8034 (mttp) cc_final: 0.7367 (tptp) REVERT: A 572 LYS cc_start: 0.7879 (pttt) cc_final: 0.7376 (pptt) REVERT: C 14 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7667 (mp) REVERT: C 45 LYS cc_start: 0.7202 (mmtt) cc_final: 0.6345 (mtpp) REVERT: C 100 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.5005 (ptp-170) REVERT: D 329 LYS cc_start: 0.8009 (mttp) cc_final: 0.7321 (tptp) REVERT: F 14 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7658 (mp) REVERT: F 45 LYS cc_start: 0.7213 (mmtt) cc_final: 0.6368 (mtpp) REVERT: F 100 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.5025 (ptp-170) outliers start: 45 outliers final: 29 residues processed: 226 average time/residue: 0.4941 time to fit residues: 165.0980 Evaluate side-chains 226 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 193 time to evaluate : 1.946 ------------------------------------------------------------------------------- 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 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 540 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 34 TYR Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 0.9990 chunk 133 optimal weight: 0.4980 chunk 141 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 128 optimal weight: 0.0970 chunk 134 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.5687 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= 0.224 Angle : 0.562 6.021 17196 Z= 0.298 Chirality : 0.045 0.169 1930 Planarity : 0.005 0.046 2196 Dihedral : 4.674 22.095 1686 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.45 % Allowed : 11.10 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.21), residues: 1542 helix: 1.13 (0.40), residues: 178 sheet: -0.41 (0.21), residues: 574 loop : -0.81 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 658 HIS 0.002 0.001 HIS D 245 PHE 0.011 0.001 PHE A 629 TYR 0.014 0.002 TYR E 49 ARG 0.003 0.000 ARG B 66 *********************** 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 227 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 193 time to evaluate : 1.990 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: 0.4602 (mtp) cc_final: 0.2605 (tpt) REVERT: A 329 LYS cc_start: 0.7995 (mttp) cc_final: 0.7299 (tptp) REVERT: A 572 LYS cc_start: 0.7873 (pttt) cc_final: 0.7340 (pptt) REVERT: C 14 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7692 (mp) REVERT: C 45 LYS cc_start: 0.7214 (mmtt) cc_final: 0.6330 (mtpp) REVERT: C 100 ARG cc_start: 0.6896 (OUTLIER) cc_final: 0.5004 (ptp-170) REVERT: D 329 LYS cc_start: 0.7981 (mttp) cc_final: 0.7288 (tptp) REVERT: F 14 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7654 (mp) REVERT: F 45 LYS cc_start: 0.7237 (mmtt) cc_final: 0.6338 (mtpp) REVERT: F 100 ARG cc_start: 0.6896 (OUTLIER) cc_final: 0.5000 (ptp-170) outliers start: 34 outliers final: 29 residues processed: 210 average time/residue: 0.5189 time to fit residues: 159.6607 Evaluate side-chains 218 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 185 time to evaluate : 1.834 ------------------------------------------------------------------------------- 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 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 B residue 20 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 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 208 MET 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 590 LEU Chi-restraints excluded: chain D residue 627 CYS 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 50 VAL 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 91 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 157 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 133 optimal weight: 0.0030 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12672 Z= 0.240 Angle : 0.569 9.191 17196 Z= 0.301 Chirality : 0.045 0.167 1930 Planarity : 0.005 0.047 2196 Dihedral : 4.654 24.946 1686 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.23 % Allowed : 11.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.21), residues: 1542 helix: 1.10 (0.40), residues: 178 sheet: -0.43 (0.21), residues: 578 loop : -0.95 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 658 HIS 0.002 0.001 HIS D 245 PHE 0.011 0.001 PHE A 629 TYR 0.017 0.002 TYR E 55 ARG 0.003 0.000 ARG B 66 ********************** 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 219 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 188 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 LYS cc_start: 0.8032 (mttp) cc_final: 0.7360 (tptp) REVERT: A 485 LYS cc_start: 0.7774 (mmtt) cc_final: 0.7465 (mmtm) REVERT: A 572 LYS cc_start: 0.7841 (pttt) cc_final: 0.7324 (pptt) REVERT: C 14 LEU cc_start: 0.8047 (tt) cc_final: 0.7701 (mp) REVERT: C 45 LYS cc_start: 0.7231 (mmtt) cc_final: 0.6367 (mtpp) REVERT: D 329 LYS cc_start: 0.7984 (mttp) cc_final: 0.7288 (tptp) REVERT: F 14 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7694 (mp) REVERT: F 45 LYS cc_start: 0.7222 (mmtt) cc_final: 0.6359 (mtpp) outliers start: 31 outliers final: 28 residues processed: 207 average time/residue: 0.5109 time to fit residues: 154.8648 Evaluate side-chains 214 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 185 time to evaluate : 1.838 ------------------------------------------------------------------------------- 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 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 B residue 20 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 34 TYR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 125 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 128 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN D 196 ASN D 438 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.178500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.137461 restraints weight = 36803.836| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.62 r_work: 0.3718 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12672 Z= 0.216 Angle : 0.547 4.354 17196 Z= 0.290 Chirality : 0.045 0.167 1930 Planarity : 0.005 0.046 2196 Dihedral : 4.568 21.252 1686 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.38 % Allowed : 11.53 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.21), residues: 1542 helix: 1.23 (0.40), residues: 178 sheet: -0.40 (0.21), residues: 578 loop : -0.88 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 658 HIS 0.003 0.001 HIS D 444 PHE 0.010 0.001 PHE D 629 TYR 0.015 0.002 TYR E 49 ARG 0.003 0.000 ARG E 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6413.08 seconds wall clock time: 113 minutes 16.84 seconds (6796.84 seconds total)