Starting phenix.real_space_refine on Wed Aug 5 14:16:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tik_55959/08_2026/9tik_55959.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tik_55959/08_2026/9tik_55959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tik_55959/08_2026/9tik_55959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tik_55959/08_2026/9tik_55959.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tik_55959/08_2026/9tik_55959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tik_55959/08_2026/9tik_55959.map" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 6150 2.51 5 N 1632 2.21 5 O 1968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9786 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2264 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain: "B" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2264 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain: "C" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2264 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain: "D" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 998 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "E" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 998 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "F" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 998 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Time building chain proxies: 2.14, per 1000 atoms: 0.22 Number of scatterers: 9786 At special positions: 0 Unit cell: (116.704, 115.037, 130.042, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1968 8.00 N 1632 7.00 C 6150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 322.9 milliseconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2310 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 24 sheets defined 16.1% alpha, 42.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 34 through 48 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 81 through 86 Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 259 through 272 removed outlier: 3.688A pdb=" N ARG A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'B' and resid 35 through 48 removed outlier: 3.854A pdb=" N LYS B 47 " --> pdb=" O TYR B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 72 Processing helix chain 'B' and resid 81 through 88 removed outlier: 3.503A pdb=" N LEU B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 228 through 236 removed outlier: 5.163A pdb=" N LYS B 234 " --> pdb=" O ASP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.705A pdb=" N LEU B 307 " --> pdb=" O THR B 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 48 removed outlier: 3.886A pdb=" N LYS C 47 " --> pdb=" O TYR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 81 through 86 Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 228 through 236 removed outlier: 4.530A pdb=" N LYS C 234 " --> pdb=" O ASP C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 257 Processing helix chain 'C' and resid 259 through 272 removed outlier: 3.631A pdb=" N ARG C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'D' and resid 552 through 554 No H-bonds generated for 'chain 'D' and resid 552 through 554' Processing helix chain 'E' and resid 537 through 541 Processing helix chain 'E' and resid 552 through 554 No H-bonds generated for 'chain 'E' and resid 552 through 554' Processing helix chain 'F' and resid 537 through 541 Processing helix chain 'F' and resid 552 through 554 No H-bonds generated for 'chain 'F' and resid 552 through 554' Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 80 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 80 removed outlier: 4.362A pdb=" N MET A 128 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 148 removed outlier: 4.280A pdb=" N MET C 128 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 148 removed outlier: 4.280A pdb=" N MET C 128 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 153 through 155 removed outlier: 4.229A pdb=" N ALA A 153 " --> pdb=" O VAL A 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 240 Processing sheet with id=AA7, first strand: chain 'A' and resid 250 through 252 removed outlier: 6.660A pdb=" N LEU A 250 " --> pdb=" O TYR A 279 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 80 Processing sheet with id=AA9, first strand: chain 'B' and resid 76 through 80 removed outlier: 4.308A pdb=" N MET B 128 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 153 through 155 removed outlier: 4.270A pdb=" N ALA B 153 " --> pdb=" O VAL B 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 239 through 240 Processing sheet with id=AB3, first strand: chain 'B' and resid 251 through 252 Processing sheet with id=AB4, first strand: chain 'C' and resid 153 through 155 removed outlier: 4.113A pdb=" N ALA C 153 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 239 through 240 Processing sheet with id=AB6, first strand: chain 'C' and resid 250 through 252 removed outlier: 6.748A pdb=" N LEU C 250 " --> pdb=" O TYR C 279 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 516 through 525 removed outlier: 5.268A pdb=" N LEU D 518 " --> pdb=" O GLY D 636 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY D 636 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR D 632 " --> pdb=" O GLY D 522 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU D 524 " --> pdb=" O LYS D 630 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS D 630 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N VAL D 631 " --> pdb=" O TRP D 549 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP D 549 " --> pdb=" O VAL D 631 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN D 633 " --> pdb=" O THR D 547 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR D 550 " --> pdb=" O HIS D 555 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS D 555 " --> pdb=" O THR D 550 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 532 through 533 removed outlier: 7.749A pdb=" N VAL D 601 " --> pdb=" O PRO D 596 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR D 594 " --> pdb=" O PRO D 603 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 532 through 533 removed outlier: 6.868A pdb=" N VAL D 606 " --> pdb=" O TRP D 623 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TRP D 623 " --> pdb=" O VAL D 606 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N SER D 608 " --> pdb=" O ALA D 621 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 516 through 525 removed outlier: 5.273A pdb=" N LEU E 518 " --> pdb=" O GLY E 636 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLY E 636 " --> pdb=" O LEU E 518 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR E 632 " --> pdb=" O GLY E 522 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU E 524 " --> pdb=" O LYS E 630 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS E 630 " --> pdb=" O LEU E 524 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VAL E 631 " --> pdb=" O TRP E 549 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N TRP E 549 " --> pdb=" O VAL E 631 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN E 633 " --> pdb=" O THR E 547 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR E 550 " --> pdb=" O HIS E 555 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N HIS E 555 " --> pdb=" O THR E 550 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 532 through 533 removed outlier: 7.788A pdb=" N VAL E 601 " --> pdb=" O PRO E 596 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N THR E 594 " --> pdb=" O PRO E 603 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 532 through 533 removed outlier: 6.788A pdb=" N VAL E 606 " --> pdb=" O TRP E 623 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP E 623 " --> pdb=" O VAL E 606 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N SER E 608 " --> pdb=" O ALA E 621 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR E 617 " --> pdb=" O ASP E 612 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 516 through 525 removed outlier: 6.537A pdb=" N ILE F 634 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS F 521 " --> pdb=" O TYR F 632 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N TYR F 632 " --> pdb=" O LYS F 521 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR F 523 " --> pdb=" O LYS F 630 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N LYS F 630 " --> pdb=" O THR F 523 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL F 631 " --> pdb=" O TRP F 549 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N TRP F 549 " --> pdb=" O VAL F 631 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN F 633 " --> pdb=" O THR F 547 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR F 550 " --> pdb=" O HIS F 555 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS F 555 " --> pdb=" O THR F 550 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 532 through 533 removed outlier: 6.723A pdb=" N SER F 600 " --> pdb=" O PRO F 596 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N TYR F 592 " --> pdb=" O GLY F 604 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL F 606 " --> pdb=" O GLU F 590 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLU F 590 " --> pdb=" O VAL F 606 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER F 608 " --> pdb=" O PHE F 588 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE F 588 " --> pdb=" O SER F 608 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N THR F 610 " --> pdb=" O VAL F 586 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL F 586 " --> pdb=" O THR F 610 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 532 through 533 removed outlier: 6.832A pdb=" N VAL F 606 " --> pdb=" O TRP F 623 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TRP F 623 " --> pdb=" O VAL F 606 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N SER F 608 " --> pdb=" O ALA F 621 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR F 617 " --> pdb=" O ASP F 612 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1107 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.58 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2490 1.33 - 1.45: 2047 1.45 - 1.58: 5371 1.58 - 1.70: 1 1.70 - 1.82: 66 Bond restraints: 9975 Sorted by residual: bond pdb=" CA GLY A 173 " pdb=" C GLY A 173 " ideal model delta sigma weight residual 1.511 1.565 -0.053 1.25e-02 6.40e+03 1.83e+01 bond pdb=" CA GLU A 228 " pdb=" C GLU A 228 " ideal model delta sigma weight residual 1.520 1.558 -0.038 1.02e-02 9.61e+03 1.37e+01 bond pdb=" CA GLU C 228 " pdb=" C GLU C 228 " ideal model delta sigma weight residual 1.520 1.557 -0.036 9.90e-03 1.02e+04 1.34e+01 bond pdb=" CD2 HIS F 555 " pdb=" NE2 HIS F 555 " ideal model delta sigma weight residual 1.374 1.412 -0.038 1.10e-02 8.26e+03 1.20e+01 bond pdb=" CZ ARG C 131 " pdb=" NH2 ARG C 131 " ideal model delta sigma weight residual 1.330 1.285 0.045 1.30e-02 5.92e+03 1.19e+01 ... (remaining 9970 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 10144 2.10 - 4.20: 2982 4.20 - 6.29: 350 6.29 - 8.39: 46 8.39 - 10.49: 5 Bond angle restraints: 13527 Sorted by residual: angle pdb=" CA ASP A 266 " pdb=" CB ASP A 266 " pdb=" CG ASP A 266 " ideal model delta sigma weight residual 112.60 119.67 -7.07 1.00e+00 1.00e+00 5.00e+01 angle pdb=" CA ASP B 242 " pdb=" CB ASP B 242 " pdb=" CG ASP B 242 " ideal model delta sigma weight residual 112.60 105.83 6.77 1.00e+00 1.00e+00 4.58e+01 angle pdb=" CA ASP B 266 " pdb=" CB ASP B 266 " pdb=" CG ASP B 266 " ideal model delta sigma weight residual 112.60 119.30 -6.70 1.00e+00 1.00e+00 4.49e+01 angle pdb=" CB HIS B 267 " pdb=" CG HIS B 267 " pdb=" CD2 HIS B 267 " ideal model delta sigma weight residual 131.20 122.84 8.36 1.30e+00 5.92e-01 4.13e+01 angle pdb=" CA PHE A 227 " pdb=" CB PHE A 227 " pdb=" CG PHE A 227 " ideal model delta sigma weight residual 113.80 107.43 6.37 1.00e+00 1.00e+00 4.06e+01 ... (remaining 13522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 5453 17.56 - 35.12: 366 35.12 - 52.68: 67 52.68 - 70.24: 21 70.24 - 87.80: 9 Dihedral angle restraints: 5916 sinusoidal: 2295 harmonic: 3621 Sorted by residual: dihedral pdb=" CA ASP B 195 " pdb=" C ASP B 195 " pdb=" N ASN B 196 " pdb=" CA ASN B 196 " ideal model delta harmonic sigma weight residual 180.00 150.71 29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA ASP C 195 " pdb=" C ASP C 195 " pdb=" N ASN C 196 " pdb=" CA ASN C 196 " ideal model delta harmonic sigma weight residual 180.00 150.92 29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA ASP A 195 " pdb=" C ASP A 195 " pdb=" N ASN A 196 " pdb=" CA ASN A 196 " ideal model delta harmonic sigma weight residual 180.00 151.35 28.65 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 5913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1086 0.100 - 0.200: 406 0.200 - 0.299: 45 0.299 - 0.399: 3 0.399 - 0.499: 5 Chirality restraints: 1545 Sorted by residual: chirality pdb=" CA ASN E 624 " pdb=" N ASN E 624 " pdb=" C ASN E 624 " pdb=" CB ASN E 624 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.22e+00 chirality pdb=" CA ASN F 624 " pdb=" N ASN F 624 " pdb=" C ASN F 624 " pdb=" CB ASN F 624 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.48 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" CA ASN D 616 " pdb=" N ASN D 616 " pdb=" C ASN D 616 " pdb=" CB ASN D 616 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.70e+00 ... (remaining 1542 not shown) Planarity restraints: 1731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 115 " -0.139 2.00e-02 2.50e+03 1.02e-01 1.57e+02 pdb=" CG HIS C 115 " 0.158 2.00e-02 2.50e+03 pdb=" ND1 HIS C 115 " 0.069 2.00e-02 2.50e+03 pdb=" CD2 HIS C 115 " 0.057 2.00e-02 2.50e+03 pdb=" CE1 HIS C 115 " -0.074 2.00e-02 2.50e+03 pdb=" NE2 HIS C 115 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 592 " -0.138 2.00e-02 2.50e+03 8.61e-02 1.48e+02 pdb=" CG TYR F 592 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR F 592 " 0.069 2.00e-02 2.50e+03 pdb=" CD2 TYR F 592 " 0.061 2.00e-02 2.50e+03 pdb=" CE1 TYR F 592 " 0.061 2.00e-02 2.50e+03 pdb=" CE2 TYR F 592 " 0.071 2.00e-02 2.50e+03 pdb=" CZ TYR F 592 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR F 592 " -0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 541 " 0.168 2.00e-02 2.50e+03 8.49e-02 1.44e+02 pdb=" CG TYR E 541 " -0.090 2.00e-02 2.50e+03 pdb=" CD1 TYR E 541 " -0.069 2.00e-02 2.50e+03 pdb=" CD2 TYR E 541 " -0.068 2.00e-02 2.50e+03 pdb=" CE1 TYR E 541 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR E 541 " -0.027 2.00e-02 2.50e+03 pdb=" CZ TYR E 541 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR E 541 " 0.104 2.00e-02 2.50e+03 ... (remaining 1728 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 4983 2.97 - 3.46: 9677 3.46 - 3.94: 17320 3.94 - 4.42: 19390 4.42 - 4.90: 32454 Nonbonded interactions: 83824 Sorted by model distance: nonbonded pdb=" OD2 ASP A 203 " pdb=" OG1 THR A 206 " model vdw 2.492 3.040 nonbonded pdb=" OD2 ASP B 203 " pdb=" OG1 THR B 206 " model vdw 2.511 3.040 nonbonded pdb=" OD2 ASP E 536 " pdb=" OH TYR E 541 " model vdw 2.511 3.040 nonbonded pdb=" OD2 ASP C 203 " pdb=" OG1 THR C 206 " model vdw 2.513 3.040 nonbonded pdb=" OE1 GLU A 140 " pdb=" OG SER B 149 " model vdw 2.516 3.040 ... (remaining 83819 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.560 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 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 : 0.012 0.070 9975 Z= 0.735 Angle : 1.892 10.490 13527 Z= 1.230 Chirality : 0.098 0.499 1545 Planarity : 0.024 0.363 1731 Dihedral : 13.441 87.803 3606 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.93 % Favored : 95.91 % Rotamer: Outliers : 1.44 % Allowed : 3.51 % Favored : 95.05 % Cbeta Deviations : 0.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.21), residues: 1248 helix: -2.12 (0.39), residues: 110 sheet: 0.48 (0.23), residues: 416 loop : -0.94 (0.20), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.003 ARG D 628 TYR 0.168 0.033 TYR E 541 PHE 0.131 0.023 PHE C 248 TRP 0.133 0.032 TRP F 549 HIS 0.034 0.009 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.01248 / 0.73 ( 9975) covalent geometry : angle 1.89244 / 1.23 (13527) hydrogen bonds : bond 0.14363 / 9.07 ( 411) hydrogen bonds : angle 7.99344 / 5.56 ( 1107) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.6902 (m-80) cc_final: 0.6474 (m-80) REVERT: A 49 GLN cc_start: 0.6017 (tp40) cc_final: 0.5607 (mp10) REVERT: A 55 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7707 (p0) REVERT: A 56 ASP cc_start: 0.7473 (m-30) cc_final: 0.7151 (m-30) REVERT: A 80 ILE cc_start: 0.7409 (mt) cc_final: 0.6999 (mp) REVERT: A 98 ASP cc_start: 0.8009 (m-30) cc_final: 0.7381 (m-30) REVERT: A 101 LEU cc_start: 0.8460 (tp) cc_final: 0.8205 (tp) REVERT: A 114 GLN cc_start: 0.7413 (mt0) cc_final: 0.6991 (mt0) REVERT: A 144 ILE cc_start: 0.8793 (mm) cc_final: 0.8137 (pt) REVERT: A 151 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7850 (tttp) REVERT: A 186 PHE cc_start: 0.6326 (m-80) cc_final: 0.6079 (m-80) REVERT: A 214 LYS cc_start: 0.8476 (tttm) cc_final: 0.8211 (tttt) REVERT: A 261 GLN cc_start: 0.6608 (mp10) cc_final: 0.6336 (mm-40) REVERT: A 276 PHE cc_start: 0.8767 (p90) cc_final: 0.8346 (p90) REVERT: A 289 MET cc_start: 0.8234 (ptp) cc_final: 0.7686 (tpt) REVERT: A 297 PHE cc_start: 0.8164 (t80) cc_final: 0.7929 (t80) outliers start: 4 outliers final: 0 residues processed: 104 average time/residue: 0.0527 time to fit residues: 6.3564 Evaluate side-chains 60 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.093 Evaluate side-chains 63 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 544 ILE cc_start: 0.9006 (pt) cc_final: 0.8772 (mp) REVERT: D 607 LYS cc_start: 0.5452 (tttt) cc_final: 0.4857 (tttp) REVERT: D 612 ASP cc_start: 0.5768 (t0) cc_final: 0.5557 (t0) REVERT: D 626 LYS cc_start: 0.6369 (mttt) cc_final: 0.5850 (pttm) REVERT: D 631 VAL cc_start: 0.8014 (t) cc_final: 0.7796 (p) REVERT: D 635 MET cc_start: 0.7364 (mmm) cc_final: 0.7093 (tpp) outliers start: 2 outliers final: 0 residues processed: 62 average time/residue: 0.0637 time to fit residues: 4.2473 Evaluate side-chains 34 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.3980 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0270 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 0.0170 overall best weight: 0.3074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 HIS A 262 GLN A 320 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.082538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.073788 restraints weight = 9690.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.076107 restraints weight = 5531.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.077640 restraints weight = 3514.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.078734 restraints weight = 2394.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.079454 restraints weight = 1712.094| |-----------------------------------------------------------------------------| r_work (final): 0.3317 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.104188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.091842 restraints weight = 3379.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.094511 restraints weight = 2211.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.096625 restraints weight = 1535.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.098232 restraints weight = 1110.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.099368 restraints weight = 824.216| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 moved from start: 0.8212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9975 Z= 0.171 Angle : 0.706 7.727 13527 Z= 0.392 Chirality : 0.047 0.173 1545 Planarity : 0.005 0.047 1731 Dihedral : 5.451 23.974 1362 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.27 % Allowed : 4.32 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.22), residues: 1248 helix: 0.06 (0.46), residues: 123 sheet: 0.81 (0.23), residues: 450 loop : 0.01 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 639 TYR 0.020 0.002 TYR B 78 PHE 0.023 0.002 PHE A 227 TRP 0.034 0.003 TRP D 623 HIS 0.004 0.001 HIS C 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 ( 9975) covalent geometry : angle 0.70624 / 0.39 (13527) hydrogen bonds : bond 0.05261 / 3.49 ( 411) hydrogen bonds : angle 6.25927 / 4.38 ( 1107) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.7781 (mt) cc_final: 0.7265 (mp) REVERT: A 91 ARG cc_start: 0.8311 (ptt180) cc_final: 0.8100 (ptt90) REVERT: A 101 LEU cc_start: 0.8287 (tp) cc_final: 0.8002 (tp) REVERT: A 125 GLN cc_start: 0.8425 (mp-120) cc_final: 0.7866 (mp10) REVERT: A 130 TYR cc_start: 0.8048 (p90) cc_final: 0.7021 (p90) REVERT: A 160 ILE cc_start: 0.7469 (pt) cc_final: 0.6862 (pt) REVERT: A 232 MET cc_start: 0.8243 (ttm) cc_final: 0.8011 (tmm) REVERT: A 276 PHE cc_start: 0.8557 (p90) cc_final: 0.8156 (p90) REVERT: A 289 MET cc_start: 0.8258 (ptp) cc_final: 0.7472 (tmm) REVERT: A 296 LEU cc_start: 0.7547 (tp) cc_final: 0.6858 (tp) REVERT: A 298 MET cc_start: 0.9008 (mpp) cc_final: 0.8387 (mpp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0586 time to fit residues: 5.8262 Evaluate side-chains 48 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.080 Evaluate side-chains 62 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.034 Fit side-chains REVERT: F 525 ASP cc_start: 0.6801 (p0) cc_final: 0.5769 (p0) REVERT: F 537 SER cc_start: 0.7912 (t) cc_final: 0.7144 (t) REVERT: F 539 ASP cc_start: 0.8547 (m-30) cc_final: 0.8152 (m-30) REVERT: F 540 ASN cc_start: 0.7948 (m110) cc_final: 0.7248 (m110) REVERT: F 541 TYR cc_start: 0.6957 (m-80) cc_final: 0.6296 (m-80) REVERT: F 552 SER cc_start: 0.7492 (m) cc_final: 0.6942 (t) REVERT: F 557 SER cc_start: 0.7903 (m) cc_final: 0.7441 (t) REVERT: F 558 THR cc_start: 0.8614 (p) cc_final: 0.8311 (t) REVERT: F 605 MET cc_start: 0.8003 (ttp) cc_final: 0.7611 (tmm) REVERT: F 627 GLU cc_start: 0.8350 (mp0) cc_final: 0.7066 (mp0) outliers start: 1 outliers final: 0 residues processed: 62 average time/residue: 0.0418 time to fit residues: 2.8679 Evaluate side-chains 35 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 116 optimal weight: 0.1980 chunk 3 optimal weight: 2.9990 chunk 90 optimal weight: 0.0000 chunk 58 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 76 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 67.7795 > 50:) chunk 105 optimal weight: 0.0970 chunk 85 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN A 123 ASN A 125 GLN A 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.084322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.075299 restraints weight = 9835.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.077563 restraints weight = 5870.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.079088 restraints weight = 3830.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.080191 restraints weight = 2666.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.080959 restraints weight = 1933.975| |-----------------------------------------------------------------------------| r_work (final): 0.3357 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.096897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.084857 restraints weight = 3343.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.087568 restraints weight = 1979.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.089611 restraints weight = 1332.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.090946 restraints weight = 956.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.092035 restraints weight = 730.331| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 moved from start: 0.9212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9975 Z= 0.140 Angle : 0.689 10.838 13527 Z= 0.379 Chirality : 0.047 0.206 1545 Planarity : 0.004 0.035 1731 Dihedral : 5.146 24.023 1362 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.23), residues: 1248 helix: 0.57 (0.47), residues: 123 sheet: 0.76 (0.25), residues: 423 loop : 0.21 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 639 TYR 0.020 0.002 TYR C 235 PHE 0.028 0.003 PHE D 575 TRP 0.018 0.002 TRP C 223 HIS 0.004 0.001 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 9975) covalent geometry : angle 0.68914 / 0.38 (13527) hydrogen bonds : bond 0.04638 / 3.06 ( 411) hydrogen bonds : angle 5.86941 / 4.06 ( 1107) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.7915 (mt) cc_final: 0.7536 (mp) REVERT: A 98 ASP cc_start: 0.8472 (m-30) cc_final: 0.8269 (m-30) REVERT: A 101 LEU cc_start: 0.8465 (tp) cc_final: 0.8239 (tp) REVERT: A 114 GLN cc_start: 0.8247 (mt0) cc_final: 0.7355 (mm110) REVERT: A 117 TYR cc_start: 0.6976 (m-10) cc_final: 0.6716 (m-10) REVERT: A 125 GLN cc_start: 0.8201 (mp10) cc_final: 0.7873 (mp10) REVERT: A 130 TYR cc_start: 0.8031 (p90) cc_final: 0.5916 (p90) REVERT: A 144 ILE cc_start: 0.8859 (pt) cc_final: 0.8607 (pt) REVERT: A 145 GLN cc_start: 0.8110 (pp30) cc_final: 0.7881 (tm-30) REVERT: A 162 ASP cc_start: 0.7029 (m-30) cc_final: 0.6732 (m-30) REVERT: A 186 PHE cc_start: 0.6933 (m-10) cc_final: 0.6614 (m-80) REVERT: A 275 THR cc_start: 0.8393 (p) cc_final: 0.7917 (p) REVERT: A 276 PHE cc_start: 0.8716 (p90) cc_final: 0.8414 (p90) REVERT: A 289 MET cc_start: 0.8119 (ptp) cc_final: 0.7223 (tmm) REVERT: A 296 LEU cc_start: 0.7469 (tp) cc_final: 0.6979 (tp) REVERT: A 298 MET cc_start: 0.9165 (mpp) cc_final: 0.8745 (mpp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0565 time to fit residues: 5.1448 Evaluate side-chains 53 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.081 Evaluate side-chains 46 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.035 Fit side-chains REVERT: F 525 ASP cc_start: 0.7554 (p0) cc_final: 0.7000 (p0) REVERT: F 540 ASN cc_start: 0.7610 (m110) cc_final: 0.7220 (m110) REVERT: F 548 TYR cc_start: 0.7653 (p90) cc_final: 0.7028 (p90) REVERT: F 557 SER cc_start: 0.7913 (m) cc_final: 0.7615 (t) REVERT: F 590 GLU cc_start: 0.6583 (tp30) cc_final: 0.5854 (pm20) REVERT: F 605 MET cc_start: 0.8113 (ttp) cc_final: 0.7669 (tmm) REVERT: F 627 GLU cc_start: 0.7935 (mp0) cc_final: 0.7496 (mp0) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0462 time to fit residues: 2.3686 Evaluate side-chains 34 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.0000 chunk 32 optimal weight: 0.9980 chunk 55 optimal weight: 0.0270 chunk 115 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 overall best weight: 0.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN ** A 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.085604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.076650 restraints weight = 10193.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.078944 restraints weight = 6138.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.080528 restraints weight = 4016.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.081615 restraints weight = 2784.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.082405 restraints weight = 2021.390| |-----------------------------------------------------------------------------| r_work (final): 0.3375 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.098672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.085926 restraints weight = 3121.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.088673 restraints weight = 1943.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.090669 restraints weight = 1335.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.092182 restraints weight = 976.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.093045 restraints weight = 743.646| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.9442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9975 Z= 0.131 Angle : 0.633 6.515 13527 Z= 0.354 Chirality : 0.046 0.190 1545 Planarity : 0.004 0.046 1731 Dihedral : 4.946 21.480 1362 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.23), residues: 1248 helix: 0.40 (0.47), residues: 123 sheet: 0.80 (0.24), residues: 435 loop : 0.35 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 573 TYR 0.017 0.002 TYR C 235 PHE 0.014 0.002 PHE A 227 TRP 0.013 0.002 TRP C 223 HIS 0.003 0.001 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 9975) covalent geometry : angle 0.63255 / 0.35 (13527) hydrogen bonds : bond 0.04473 / 2.95 ( 411) hydrogen bonds : angle 5.83472 / 4.00 ( 1107) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7705 (tp) cc_final: 0.7473 (pp) REVERT: A 125 GLN cc_start: 0.8320 (mp10) cc_final: 0.8031 (mp10) REVERT: A 162 ASP cc_start: 0.7181 (m-30) cc_final: 0.6942 (m-30) REVERT: A 226 GLU cc_start: 0.7519 (mm-30) cc_final: 0.6821 (pt0) REVERT: A 289 MET cc_start: 0.8163 (ptp) cc_final: 0.7275 (tmm) REVERT: A 296 LEU cc_start: 0.7433 (tp) cc_final: 0.7164 (tp) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0561 time to fit residues: 3.9798 Evaluate side-chains 44 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.057 Evaluate side-chains 41 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.030 Fit side-chains REVERT: F 525 ASP cc_start: 0.7492 (p0) cc_final: 0.6935 (p0) REVERT: F 548 TYR cc_start: 0.7878 (p90) cc_final: 0.6982 (p90) REVERT: F 557 SER cc_start: 0.7790 (m) cc_final: 0.7560 (t) REVERT: F 605 MET cc_start: 0.7569 (ttp) cc_final: 0.6945 (tmm) REVERT: F 627 GLU cc_start: 0.7816 (mp0) cc_final: 0.7397 (mp0) REVERT: F 631 VAL cc_start: 0.8902 (t) cc_final: 0.8630 (p) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0289 time to fit residues: 1.3710 Evaluate side-chains 29 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 113 optimal weight: 0.0980 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 chunk 76 optimal weight: 0.5980 chunk 43 optimal weight: 0.0670 chunk 105 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 42 optimal weight: 0.0980 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.2318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.086667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.077617 restraints weight = 9689.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.079854 restraints weight = 5910.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.081403 restraints weight = 3901.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.082520 restraints weight = 2715.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.083316 restraints weight = 1958.855| |-----------------------------------------------------------------------------| r_work (final): 0.3397 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.096239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.083906 restraints weight = 3295.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.086461 restraints weight = 1999.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.088367 restraints weight = 1373.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.089829 restraints weight = 1012.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.090898 restraints weight = 772.693| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.9639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9975 Z= 0.121 Angle : 0.640 7.280 13527 Z= 0.353 Chirality : 0.047 0.215 1545 Planarity : 0.004 0.048 1731 Dihedral : 4.842 19.891 1362 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.23), residues: 1248 helix: 0.19 (0.46), residues: 120 sheet: 0.94 (0.24), residues: 435 loop : 0.32 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 573 TYR 0.013 0.001 TYR C 235 PHE 0.012 0.002 PHE C 143 TRP 0.022 0.002 TRP C 223 HIS 0.002 0.001 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 9975) covalent geometry : angle 0.64010 / 0.35 (13527) hydrogen bonds : bond 0.04499 / 2.93 ( 411) hydrogen bonds : angle 5.77965 / 3.95 ( 1107) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASP cc_start: 0.7435 (t0) cc_final: 0.6720 (m-30) REVERT: A 97 LEU cc_start: 0.7720 (tp) cc_final: 0.7382 (pp) REVERT: A 103 VAL cc_start: 0.8227 (t) cc_final: 0.7988 (t) REVERT: A 113 VAL cc_start: 0.8865 (t) cc_final: 0.8596 (t) REVERT: A 130 TYR cc_start: 0.7775 (p90) cc_final: 0.5678 (p90) REVERT: A 162 ASP cc_start: 0.7636 (m-30) cc_final: 0.7326 (m-30) REVERT: A 296 LEU cc_start: 0.6993 (tp) cc_final: 0.6514 (tp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0540 time to fit residues: 4.1695 Evaluate side-chains 44 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.064 Evaluate side-chains 38 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.040 Fit side-chains REVERT: F 518 LEU cc_start: 0.8638 (mm) cc_final: 0.8224 (mt) REVERT: F 525 ASP cc_start: 0.7204 (p0) cc_final: 0.6551 (p0) REVERT: F 548 TYR cc_start: 0.8003 (p90) cc_final: 0.7117 (p90) REVERT: F 627 GLU cc_start: 0.7473 (mp0) cc_final: 0.7122 (mp0) REVERT: F 631 VAL cc_start: 0.8816 (t) cc_final: 0.8556 (p) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0398 time to fit residues: 1.7198 Evaluate side-chains 29 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 106 optimal weight: 0.0270 chunk 69 optimal weight: 0.3980 chunk 42 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 0.0020 chunk 91 optimal weight: 0.0170 chunk 72 optimal weight: 0.5980 overall best weight: 0.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS A 262 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.086905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.078349 restraints weight = 10145.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.080596 restraints weight = 6057.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.082094 restraints weight = 3960.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.083142 restraints weight = 2729.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.083858 restraints weight = 1968.915| |-----------------------------------------------------------------------------| r_work (final): 0.3407 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.098809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.085004 restraints weight = 3075.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.087875 restraints weight = 1864.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.089958 restraints weight = 1277.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.091501 restraints weight = 932.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.092715 restraints weight = 712.852| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.9892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9975 Z= 0.139 Angle : 0.686 8.650 13527 Z= 0.375 Chirality : 0.046 0.156 1545 Planarity : 0.005 0.058 1731 Dihedral : 5.100 20.145 1362 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.23), residues: 1248 helix: -0.09 (0.45), residues: 120 sheet: 0.86 (0.24), residues: 435 loop : 0.33 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 573 TYR 0.014 0.002 TYR B 117 PHE 0.038 0.002 PHE A 227 TRP 0.014 0.002 TRP E 549 HIS 0.002 0.001 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 9975) covalent geometry : angle 0.68597 / 0.37 (13527) hydrogen bonds : bond 0.04710 / 3.04 ( 411) hydrogen bonds : angle 6.01848 / 4.10 ( 1107) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 VAL cc_start: 0.8965 (t) cc_final: 0.8752 (t) REVERT: A 125 GLN cc_start: 0.8114 (mp10) cc_final: 0.7871 (mp10) REVERT: A 209 GLU cc_start: 0.8585 (pp20) cc_final: 0.8038 (pp20) REVERT: A 296 LEU cc_start: 0.6746 (tp) cc_final: 0.6290 (tp) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0595 time to fit residues: 4.2557 Evaluate side-chains 44 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.087 Evaluate side-chains 40 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.037 Fit side-chains revert: symmetry clash REVERT: F 525 ASP cc_start: 0.7080 (p0) cc_final: 0.6544 (p0) REVERT: F 534 LEU cc_start: 0.8242 (mt) cc_final: 0.7962 (mt) REVERT: F 548 TYR cc_start: 0.8190 (p90) cc_final: 0.7669 (p90) REVERT: F 575 PHE cc_start: 0.6305 (p90) cc_final: 0.6069 (p90) REVERT: F 627 GLU cc_start: 0.7448 (mp0) cc_final: 0.6973 (mp0) REVERT: F 631 VAL cc_start: 0.8603 (t) cc_final: 0.8399 (p) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0343 time to fit residues: 1.5525 Evaluate side-chains 30 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 17 optimal weight: 0.8980 chunk 110 optimal weight: 0.0170 chunk 64 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 73 optimal weight: 0.0570 chunk 53 optimal weight: 0.3980 chunk 106 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 0.1980 chunk 77 optimal weight: 0.0070 chunk 7 optimal weight: 0.0020 overall best weight: 0.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.086737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.077990 restraints weight = 9969.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.080159 restraints weight = 6058.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.081593 restraints weight = 4025.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.082646 restraints weight = 2845.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.083420 restraints weight = 2071.746| |-----------------------------------------------------------------------------| r_work (final): 0.3406 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.099863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.085245 restraints weight = 3317.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.087954 restraints weight = 2129.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.089963 restraints weight = 1511.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.091605 restraints weight = 1141.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.092809 restraints weight = 891.327| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 1.0169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9975 Z= 0.140 Angle : 0.700 8.532 13527 Z= 0.382 Chirality : 0.046 0.176 1545 Planarity : 0.005 0.066 1731 Dihedral : 4.996 25.484 1362 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.24), residues: 1248 helix: -0.02 (0.45), residues: 120 sheet: 0.87 (0.25), residues: 435 loop : 0.39 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 573 TYR 0.013 0.001 TYR A 235 PHE 0.021 0.002 PHE C 227 TRP 0.019 0.002 TRP A 223 HIS 0.002 0.001 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 9975) covalent geometry : angle 0.70006 / 0.38 (13527) hydrogen bonds : bond 0.04466 / 2.91 ( 411) hydrogen bonds : angle 5.96720 / 4.04 ( 1107) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8328 (mp10) cc_final: 0.8025 (mp10) REVERT: A 130 TYR cc_start: 0.7070 (p90) cc_final: 0.5704 (p90) REVERT: A 186 PHE cc_start: 0.7498 (m-80) cc_final: 0.7278 (m-80) REVERT: A 209 GLU cc_start: 0.8570 (pp20) cc_final: 0.8033 (pp20) REVERT: A 296 LEU cc_start: 0.6738 (tp) cc_final: 0.6280 (tp) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0549 time to fit residues: 3.7853 Evaluate side-chains 43 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.081 Evaluate side-chains 38 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.036 Fit side-chains revert: symmetry clash REVERT: F 541 TYR cc_start: 0.6845 (m-80) cc_final: 0.6626 (m-80) REVERT: F 561 LEU cc_start: 0.7180 (mm) cc_final: 0.6896 (mm) REVERT: F 627 GLU cc_start: 0.7007 (mp0) cc_final: 0.6015 (mp0) REVERT: F 631 VAL cc_start: 0.8541 (t) cc_final: 0.8143 (p) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0391 time to fit residues: 1.6906 Evaluate side-chains 25 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 45 optimal weight: 0.0270 chunk 74 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 97 optimal weight: 0.0060 chunk 75 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.4454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.087070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.078108 restraints weight = 10478.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.080337 restraints weight = 6414.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.081667 restraints weight = 4277.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.082828 restraints weight = 3092.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.083618 restraints weight = 2272.859| |-----------------------------------------------------------------------------| r_work (final): 0.3403 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.100200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.085604 restraints weight = 3064.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.088465 restraints weight = 1919.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.090702 restraints weight = 1344.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.092430 restraints weight = 998.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.093695 restraints weight = 765.612| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 1.0318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9975 Z= 0.138 Angle : 0.684 11.535 13527 Z= 0.372 Chirality : 0.048 0.232 1545 Planarity : 0.006 0.082 1731 Dihedral : 4.999 31.358 1362 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.24), residues: 1248 helix: 0.05 (0.46), residues: 120 sheet: 0.64 (0.25), residues: 471 loop : 0.40 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 573 TYR 0.010 0.002 TYR C 117 PHE 0.017 0.001 PHE B 227 TRP 0.013 0.002 TRP A 223 HIS 0.004 0.001 HIS C 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 9975) covalent geometry : angle 0.68388 / 0.37 (13527) hydrogen bonds : bond 0.04728 / 3.10 ( 411) hydrogen bonds : angle 6.17440 / 4.18 ( 1107) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8365 (mp10) cc_final: 0.8058 (mp10) REVERT: A 128 MET cc_start: 0.5516 (mmt) cc_final: 0.4527 (mmt) REVERT: A 186 PHE cc_start: 0.7531 (m-80) cc_final: 0.7329 (m-80) REVERT: A 209 GLU cc_start: 0.8601 (pp20) cc_final: 0.8065 (pp20) REVERT: A 277 THR cc_start: 0.8534 (p) cc_final: 0.7867 (p) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0555 time to fit residues: 3.9930 Evaluate side-chains 45 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.081 Evaluate side-chains 40 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.041 Fit side-chains revert: symmetry clash REVERT: F 541 TYR cc_start: 0.6743 (m-80) cc_final: 0.6458 (m-80) REVERT: F 568 ASN cc_start: 0.4007 (m-40) cc_final: 0.3767 (m-40) REVERT: F 633 ASN cc_start: 0.7840 (p0) cc_final: 0.7232 (p0) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0376 time to fit residues: 1.7296 Evaluate side-chains 25 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 46 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 99 optimal weight: 0.0070 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 0.4980 chunk 91 optimal weight: 0.0570 chunk 59 optimal weight: 0.7980 chunk 105 optimal weight: 0.0070 overall best weight: 0.2134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.088601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.079811 restraints weight = 9973.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.082046 restraints weight = 6129.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.083597 restraints weight = 4058.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.084467 restraints weight = 2837.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.085274 restraints weight = 2135.022| |-----------------------------------------------------------------------------| r_work (final): 0.3441 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.100353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.087068 restraints weight = 3124.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.090086 restraints weight = 1886.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.092195 restraints weight = 1266.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.093649 restraints weight = 909.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.094812 restraints weight = 686.202| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 1.0599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9975 Z= 0.143 Angle : 0.700 8.508 13527 Z= 0.380 Chirality : 0.049 0.213 1545 Planarity : 0.005 0.076 1731 Dihedral : 5.011 33.833 1362 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.24), residues: 1248 helix: -0.25 (0.48), residues: 120 sheet: 1.00 (0.26), residues: 441 loop : 0.18 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 628 TYR 0.017 0.001 TYR D 548 PHE 0.032 0.002 PHE F 575 TRP 0.009 0.002 TRP B 141 HIS 0.003 0.001 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 9975) covalent geometry : angle 0.69956 / 0.38 (13527) hydrogen bonds : bond 0.04671 / 3.08 ( 411) hydrogen bonds : angle 6.42114 / 4.34 ( 1107) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TYR cc_start: 0.6870 (p90) cc_final: 0.6299 (p90) REVERT: A 147 LEU cc_start: 0.8015 (pt) cc_final: 0.7652 (mt) REVERT: A 162 ASP cc_start: 0.7759 (m-30) cc_final: 0.7555 (m-30) REVERT: A 209 GLU cc_start: 0.8586 (pp20) cc_final: 0.7819 (pp20) REVERT: A 310 VAL cc_start: 0.8646 (p) cc_final: 0.8410 (t) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0627 time to fit residues: 4.2877 Evaluate side-chains 43 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.086 Evaluate side-chains 38 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.038 Fit side-chains revert: symmetry clash REVERT: F 534 LEU cc_start: 0.8527 (mt) cc_final: 0.8327 (mt) REVERT: F 537 SER cc_start: 0.8148 (t) cc_final: 0.7261 (p) REVERT: F 545 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7148 (pt0) REVERT: F 568 ASN cc_start: 0.3812 (m-40) cc_final: 0.3330 (m-40) REVERT: F 587 ASP cc_start: 0.7507 (p0) cc_final: 0.7285 (p0) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0400 time to fit residues: 1.7260 Evaluate side-chains 27 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 43 optimal weight: 0.0970 chunk 97 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 122 optimal weight: 0.0570 chunk 101 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 74 optimal weight: 0.1980 chunk 38 optimal weight: 0.0270 overall best weight: 0.2354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 540 ASN F 555 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.089424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.080982 restraints weight = 9997.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.083172 restraints weight = 6013.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.084646 restraints weight = 3947.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.085633 restraints weight = 2749.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.086379 restraints weight = 2009.644| |-----------------------------------------------------------------------------| r_work (final): 0.3463 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.100553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.086477 restraints weight = 3309.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.089583 restraints weight = 2047.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.091806 restraints weight = 1387.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.093404 restraints weight = 1006.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.094644 restraints weight = 765.702| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 1.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9975 Z= 0.140 Angle : 0.724 8.617 13527 Z= 0.395 Chirality : 0.048 0.215 1545 Planarity : 0.005 0.070 1731 Dihedral : 5.276 38.759 1362 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.24), residues: 1248 helix: -0.10 (0.48), residues: 120 sheet: 1.08 (0.25), residues: 417 loop : 0.09 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 573 TYR 0.019 0.002 TYR C 117 PHE 0.019 0.002 PHE B 248 TRP 0.030 0.003 TRP D 520 HIS 0.008 0.002 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 9975) covalent geometry : angle 0.72354 / 0.39 (13527) hydrogen bonds : bond 0.04562 / 3.02 ( 411) hydrogen bonds : angle 6.37886 / 4.30 ( 1107) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASP cc_start: 0.7181 (t0) cc_final: 0.6737 (m-30) REVERT: A 125 GLN cc_start: 0.8522 (mp10) cc_final: 0.8267 (mp10) REVERT: A 130 TYR cc_start: 0.6283 (p90) cc_final: 0.3667 (p90) REVERT: A 189 LEU cc_start: 0.9311 (tp) cc_final: 0.9104 (tp) REVERT: A 209 GLU cc_start: 0.8450 (pp20) cc_final: 0.8233 (pp20) REVERT: A 226 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7334 (mp0) REVERT: A 232 MET cc_start: 0.7511 (tmm) cc_final: 0.7300 (tmm) REVERT: A 289 MET cc_start: 0.8543 (ptp) cc_final: 0.7375 (tmm) REVERT: A 314 ILE cc_start: 0.8278 (pt) cc_final: 0.7820 (mm) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0624 time to fit residues: 4.2298 Evaluate side-chains 41 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.075 Evaluate side-chains 37 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.024 Fit side-chains REVERT: F 534 LEU cc_start: 0.8552 (mt) cc_final: 0.8331 (mt) REVERT: F 545 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7117 (tt0) REVERT: F 550 THR cc_start: 0.7316 (m) cc_final: 0.6621 (p) REVERT: F 568 ASN cc_start: 0.3632 (m-40) cc_final: 0.3328 (m-40) REVERT: F 589 PHE cc_start: 0.1856 (m-10) cc_final: 0.1636 (m-10) REVERT: F 629 ILE cc_start: 0.8341 (mm) cc_final: 0.8133 (mm) REVERT: F 633 ASN cc_start: 0.7919 (p0) cc_final: 0.7162 (p0) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0281 time to fit residues: 1.1939 Evaluate side-chains 28 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 97 optimal weight: 0.9990 chunk 24 optimal weight: 0.0060 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 98 optimal weight: 0.0870 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 106 optimal weight: 0.0980 chunk 96 optimal weight: 7.9990 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.088687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.080113 restraints weight = 10452.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.082315 restraints weight = 6336.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.083821 restraints weight = 4199.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.084888 restraints weight = 2935.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.085597 restraints weight = 2133.264| |-----------------------------------------------------------------------------| r_work (final): 0.3441 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.100629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.087924 restraints weight = 3449.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.090808 restraints weight = 2080.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.092907 restraints weight = 1399.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.094320 restraints weight = 1007.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.095363 restraints weight = 762.693| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 1.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9975 Z= 0.133 Angle : 0.702 7.975 13527 Z= 0.384 Chirality : 0.047 0.186 1545 Planarity : 0.005 0.069 1731 Dihedral : 5.301 36.868 1362 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.24), residues: 1248 helix: -0.40 (0.48), residues: 120 sheet: 1.14 (0.26), residues: 414 loop : -0.06 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 91 TYR 0.026 0.002 TYR A 117 PHE 0.035 0.003 PHE C 186 TRP 0.030 0.002 TRP E 520 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 9975) covalent geometry : angle 0.70168 / 0.38 (13527) hydrogen bonds : bond 0.04548 / 2.98 ( 411) hydrogen bonds : angle 6.26430 / 4.22 ( 1107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1030.01 seconds wall clock time: 18 minutes 50.06 seconds (1130.06 seconds total)