Starting phenix.real_space_refine on Tue Jul 29 12:52:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jpr_36487/07_2025/8jpr_36487.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpr_36487/07_2025/8jpr_36487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jpr_36487/07_2025/8jpr_36487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpr_36487/07_2025/8jpr_36487.map" model { file = "/net/cci-nas-00/data/ceres_data/8jpr_36487/07_2025/8jpr_36487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpr_36487/07_2025/8jpr_36487.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.058 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 72 5.16 5 Cl 4 4.86 5 C 7368 2.51 5 N 1910 2.21 5 O 2034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11396 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5664 Classifications: {'peptide': 730} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 30, 'TRANS': 699} Chain breaks: 4 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 5664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5664 Classifications: {'peptide': 730} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 30, 'TRANS': 699} Chain breaks: 4 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CL': 2, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CL': 2, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 9.26, per 1000 atoms: 0.81 Number of scatterers: 11396 At special positions: 0 Unit cell: (96.301, 92.9514, 113.886, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 4 17.00 S 72 16.00 P 6 15.00 Mg 2 11.99 O 2034 8.00 N 1910 7.00 C 7368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 125 " distance=2.02 Simple disulfide: pdb=" SG CYS A 319 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 399 " - pdb=" SG CYS A 430 " distance=2.04 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 125 " distance=2.02 Simple disulfide: pdb=" SG CYS B 319 " - pdb=" SG CYS B 326 " distance=2.03 Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 430 " distance=2.04 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: 3.40 Conformation dependent library (CDL) restraints added in 1.6 seconds 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2684 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 8 sheets defined 65.9% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'A' and resid 58 through 68 Processing helix chain 'A' and resid 69 through 124 removed outlier: 3.660A pdb=" N GLN A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 151 removed outlier: 3.669A pdb=" N LEU A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 155 Processing helix chain 'A' and resid 158 through 168 removed outlier: 3.859A pdb=" N CYS A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 191 removed outlier: 3.687A pdb=" N LEU A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 199 through 214 removed outlier: 3.501A pdb=" N MET A 203 " --> pdb=" O LYS A 199 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 255 removed outlier: 4.001A pdb=" N ASP A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 273 through 299 removed outlier: 3.869A pdb=" N LYS A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 366 removed outlier: 3.566A pdb=" N GLY A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG A 357 " --> pdb=" O CYS A 353 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 395 Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'A' and resid 445 through 449 Processing helix chain 'A' and resid 450 through 456 Processing helix chain 'A' and resid 461 through 480 removed outlier: 4.259A pdb=" N LEU A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA A 476 " --> pdb=" O TYR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 510 removed outlier: 3.719A pdb=" N CYS A 495 " --> pdb=" O PRO A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 534 removed outlier: 3.604A pdb=" N PHE A 521 " --> pdb=" O TYR A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 554 through 569 removed outlier: 3.833A pdb=" N VAL A 563 " --> pdb=" O VAL A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 removed outlier: 3.824A pdb=" N ARG A 583 " --> pdb=" O HIS A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 removed outlier: 3.542A pdb=" N ASP A 597 " --> pdb=" O VAL A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 605 removed outlier: 3.827A pdb=" N ILE A 604 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 600 through 605' Processing helix chain 'A' and resid 618 through 628 Processing helix chain 'A' and resid 650 through 664 removed outlier: 3.623A pdb=" N ILE A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 677 Processing helix chain 'A' and resid 732 through 736 Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 773 through 778 Processing helix chain 'A' and resid 819 through 830 Processing helix chain 'A' and resid 849 through 853 Processing helix chain 'A' and resid 854 through 869 Processing helix chain 'B' and resid 58 through 68 Processing helix chain 'B' and resid 69 through 124 removed outlier: 3.651A pdb=" N GLN B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 151 removed outlier: 3.667A pdb=" N LEU B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 155 Processing helix chain 'B' and resid 158 through 168 removed outlier: 3.843A pdb=" N CYS B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR B 165 " --> pdb=" O GLU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 191 removed outlier: 3.690A pdb=" N LEU B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 199 through 214 removed outlier: 3.502A pdb=" N MET B 203 " --> pdb=" O LYS B 199 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE B 204 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 255 removed outlier: 4.004A pdb=" N ASP B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 273 through 299 removed outlier: 3.846A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 366 removed outlier: 3.565A pdb=" N GLY B 341 " --> pdb=" O PHE B 337 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG B 357 " --> pdb=" O CYS B 353 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 395 Processing helix chain 'B' and resid 436 through 443 Processing helix chain 'B' and resid 445 through 449 Processing helix chain 'B' and resid 450 through 456 Processing helix chain 'B' and resid 461 through 480 removed outlier: 4.229A pdb=" N LEU B 475 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B 476 " --> pdb=" O TYR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 510 removed outlier: 3.716A pdb=" N CYS B 495 " --> pdb=" O PRO B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 534 removed outlier: 3.582A pdb=" N PHE B 521 " --> pdb=" O TYR B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 549 Processing helix chain 'B' and resid 554 through 569 removed outlier: 3.503A pdb=" N THR B 560 " --> pdb=" O PRO B 556 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL B 563 " --> pdb=" O VAL B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 583 removed outlier: 3.827A pdb=" N ARG B 583 " --> pdb=" O HIS B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 599 Processing helix chain 'B' and resid 600 through 605 removed outlier: 3.822A pdb=" N ILE B 604 " --> pdb=" O ARG B 600 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET B 605 " --> pdb=" O ALA B 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 600 through 605' Processing helix chain 'B' and resid 618 through 628 Processing helix chain 'B' and resid 650 through 664 removed outlier: 3.621A pdb=" N ILE B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 677 Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 747 through 756 Processing helix chain 'B' and resid 773 through 778 Processing helix chain 'B' and resid 819 through 830 Processing helix chain 'B' and resid 849 through 853 Processing helix chain 'B' and resid 854 through 869 Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 401 Processing sheet with id=AA2, first strand: chain 'A' and resid 616 through 617 Processing sheet with id=AA3, first strand: chain 'A' and resid 632 through 638 removed outlier: 6.470A pdb=" N THR A 637 " --> pdb=" O PHE A 741 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N PHE A 741 " --> pdb=" O THR A 637 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 835 through 838 removed outlier: 6.786A pdb=" N LEU A 835 " --> pdb=" O ILE A 847 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE A 847 " --> pdb=" O LEU A 835 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A 837 " --> pdb=" O VAL A 845 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 400 through 401 Processing sheet with id=AA6, first strand: chain 'B' and resid 616 through 617 Processing sheet with id=AA7, first strand: chain 'B' and resid 632 through 638 removed outlier: 6.466A pdb=" N THR B 637 " --> pdb=" O PHE B 741 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N PHE B 741 " --> pdb=" O THR B 637 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 835 through 838 removed outlier: 6.787A pdb=" N LEU B 835 " --> pdb=" O ILE B 847 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE B 847 " --> pdb=" O LEU B 835 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL B 837 " --> pdb=" O VAL B 845 " (cutoff:3.500A) 676 hydrogen bonds defined for protein. 1971 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: 4.11 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3595 1.35 - 1.47: 2936 1.47 - 1.60: 5003 1.60 - 1.72: 0 1.72 - 1.85: 112 Bond restraints: 11646 Sorted by residual: bond pdb=" C TYR A 781 " pdb=" N PRO A 782 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.73e+00 bond pdb=" C TYR B 781 " pdb=" N PRO B 782 " ideal model delta sigma weight residual 1.335 1.353 -0.017 1.36e-02 5.41e+03 1.61e+00 bond pdb=" CA VAL B 758 " pdb=" CB VAL B 758 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.38e+00 bond pdb=" CB CYS A 125 " pdb=" SG CYS A 125 " ideal model delta sigma weight residual 1.808 1.845 -0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CA VAL A 758 " pdb=" CB VAL A 758 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.23e+00 ... (remaining 11641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 15491 1.62 - 3.23: 250 3.23 - 4.85: 48 4.85 - 6.46: 13 6.46 - 8.08: 2 Bond angle restraints: 15804 Sorted by residual: angle pdb=" N VAL A 169 " pdb=" CA VAL A 169 " pdb=" C VAL A 169 " ideal model delta sigma weight residual 112.96 109.14 3.82 1.00e+00 1.00e+00 1.46e+01 angle pdb=" N VAL B 169 " pdb=" CA VAL B 169 " pdb=" C VAL B 169 " ideal model delta sigma weight residual 112.96 109.17 3.79 1.00e+00 1.00e+00 1.44e+01 angle pdb=" CA CYS B 125 " pdb=" CB CYS B 125 " pdb=" SG CYS B 125 " ideal model delta sigma weight residual 114.40 122.48 -8.08 2.30e+00 1.89e-01 1.23e+01 angle pdb=" CA CYS A 125 " pdb=" CB CYS A 125 " pdb=" SG CYS A 125 " ideal model delta sigma weight residual 114.40 122.41 -8.01 2.30e+00 1.89e-01 1.21e+01 angle pdb=" N VAL B 148 " pdb=" CA VAL B 148 " pdb=" C VAL B 148 " ideal model delta sigma weight residual 112.35 108.61 3.74 1.41e+00 5.03e-01 7.03e+00 ... (remaining 15799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 6274 17.30 - 34.59: 491 34.59 - 51.89: 110 51.89 - 69.19: 10 69.19 - 86.49: 17 Dihedral angle restraints: 6902 sinusoidal: 2726 harmonic: 4176 Sorted by residual: dihedral pdb=" CB CYS B 399 " pdb=" SG CYS B 399 " pdb=" SG CYS B 430 " pdb=" CB CYS B 430 " ideal model delta sinusoidal sigma weight residual 93.00 165.01 -72.01 1 1.00e+01 1.00e-02 6.64e+01 dihedral pdb=" CB CYS B 120 " pdb=" SG CYS B 120 " pdb=" SG CYS B 125 " pdb=" CB CYS B 125 " ideal model delta sinusoidal sigma weight residual -86.00 -152.44 66.44 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CB CYS A 399 " pdb=" SG CYS A 399 " pdb=" SG CYS A 430 " pdb=" CB CYS A 430 " ideal model delta sinusoidal sigma weight residual 93.00 158.88 -65.88 1 1.00e+01 1.00e-02 5.68e+01 ... (remaining 6899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1264 0.034 - 0.068: 419 0.068 - 0.102: 98 0.102 - 0.137: 47 0.137 - 0.171: 4 Chirality restraints: 1832 Sorted by residual: chirality pdb=" CA PHE B 101 " pdb=" N PHE B 101 " pdb=" C PHE B 101 " pdb=" CB PHE B 101 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.28e-01 chirality pdb=" CA PHE A 101 " pdb=" N PHE A 101 " pdb=" C PHE A 101 " pdb=" CB PHE A 101 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CA VAL B 171 " pdb=" N VAL B 171 " pdb=" C VAL B 171 " pdb=" CB VAL B 171 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 1829 not shown) Planarity restraints: 1976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 351 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C PHE A 351 " 0.028 2.00e-02 2.50e+03 pdb=" O PHE A 351 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN A 352 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 835 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO B 836 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 836 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 836 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 835 " 0.025 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO A 836 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 836 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 836 " 0.021 5.00e-02 4.00e+02 ... (remaining 1973 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 118 2.67 - 3.23: 11180 3.23 - 3.78: 17341 3.78 - 4.34: 23438 4.34 - 4.90: 40256 Nonbonded interactions: 92333 Sorted by model distance: nonbonded pdb=" OD1 ASP A 235 " pdb=" OH TYR A 781 " model vdw 2.111 3.040 nonbonded pdb=" OD1 ASP B 235 " pdb=" OH TYR B 781 " model vdw 2.111 3.040 nonbonded pdb=" O PRO B 431 " pdb=" OG1 THR B 434 " model vdw 2.150 3.040 nonbonded pdb=" O PRO A 431 " pdb=" OG1 THR A 434 " model vdw 2.162 3.040 nonbonded pdb=" O PHE B 428 " pdb=" ND2 ASN B 436 " model vdw 2.230 3.120 ... (remaining 92328 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 46 through 869 or resid 902 or resid 904)) selection = (chain 'B' and (resid 46 through 869 or resid 902 or resid 904)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 35.020 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 : 0.003 0.037 11652 Z= 0.132 Angle : 0.559 8.080 15816 Z= 0.312 Chirality : 0.039 0.171 1832 Planarity : 0.004 0.039 1976 Dihedral : 13.514 86.486 4200 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.23), residues: 1440 helix: 1.58 (0.18), residues: 886 sheet: -4.21 (0.63), residues: 20 loop : -0.59 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 278 HIS 0.002 0.001 HIS A 834 PHE 0.023 0.001 PHE B 101 TYR 0.007 0.001 TYR A 781 ARG 0.004 0.000 ARG B 501 Details of bonding type rmsd hydrogen bonds : bond 0.14621 ( 676) hydrogen bonds : angle 6.31140 ( 1971) SS BOND : bond 0.00528 ( 6) SS BOND : angle 2.17950 ( 12) covalent geometry : bond 0.00283 (11646) covalent geometry : angle 0.55633 (15804) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 ARG cc_start: 0.7411 (mtp180) cc_final: 0.7083 (mtp85) REVERT: B 374 ARG cc_start: 0.7404 (mtp180) cc_final: 0.7077 (mtp85) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.3001 time to fit residues: 102.3130 Evaluate side-chains 121 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 444 ASN A 452 GLN A 764 GLN B 444 ASN B 764 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.136337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.110498 restraints weight = 15928.867| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.17 r_work: 0.3138 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 11652 Z= 0.222 Angle : 0.640 7.265 15816 Z= 0.330 Chirality : 0.044 0.155 1832 Planarity : 0.005 0.039 1976 Dihedral : 8.848 86.523 1632 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.29 % Allowed : 8.95 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.23), residues: 1440 helix: 1.76 (0.18), residues: 898 sheet: -4.28 (0.62), residues: 20 loop : -0.80 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 278 HIS 0.005 0.001 HIS A 455 PHE 0.018 0.002 PHE B 473 TYR 0.011 0.001 TYR A 806 ARG 0.004 0.001 ARG B 295 Details of bonding type rmsd hydrogen bonds : bond 0.04690 ( 676) hydrogen bonds : angle 4.08430 ( 1971) SS BOND : bond 0.00490 ( 6) SS BOND : angle 1.19258 ( 12) covalent geometry : bond 0.00539 (11646) covalent geometry : angle 0.63946 (15804) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 1.514 Fit side-chains REVERT: A 670 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7446 (tm-30) REVERT: A 732 MET cc_start: 0.5928 (tmm) cc_final: 0.5721 (tmm) REVERT: A 786 ASP cc_start: 0.7783 (t0) cc_final: 0.7321 (t70) REVERT: B 670 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7413 (tm-30) REVERT: B 732 MET cc_start: 0.5935 (tmm) cc_final: 0.5717 (tmm) REVERT: B 786 ASP cc_start: 0.7795 (t0) cc_final: 0.7336 (t70) outliers start: 16 outliers final: 11 residues processed: 143 average time/residue: 0.2752 time to fit residues: 57.0281 Evaluate side-chains 118 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 594 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 71 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 444 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.138965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114157 restraints weight = 15736.421| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.11 r_work: 0.3206 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11652 Z= 0.117 Angle : 0.510 7.455 15816 Z= 0.261 Chirality : 0.038 0.142 1832 Planarity : 0.004 0.033 1976 Dihedral : 8.364 82.396 1632 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.81 % Favored : 98.06 % Rotamer: Outliers : 0.81 % Allowed : 11.05 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.23), residues: 1440 helix: 2.26 (0.18), residues: 898 sheet: -4.30 (0.69), residues: 20 loop : -0.69 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 278 HIS 0.001 0.000 HIS A 615 PHE 0.010 0.001 PHE A 289 TYR 0.008 0.001 TYR A 76 ARG 0.003 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 676) hydrogen bonds : angle 3.73933 ( 1971) SS BOND : bond 0.00344 ( 6) SS BOND : angle 0.87793 ( 12) covalent geometry : bond 0.00268 (11646) covalent geometry : angle 0.50987 (15804) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 1.884 Fit side-chains REVERT: A 308 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8729 (pp) REVERT: A 332 MET cc_start: 0.6730 (tpt) cc_final: 0.6317 (mpp) REVERT: A 670 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7479 (tm-30) REVERT: B 75 ARG cc_start: 0.7758 (ttm170) cc_final: 0.7475 (ttp80) REVERT: B 308 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8737 (pp) REVERT: B 332 MET cc_start: 0.6731 (tpt) cc_final: 0.6307 (mpp) REVERT: B 670 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7475 (tm-30) REVERT: B 786 ASP cc_start: 0.7812 (t0) cc_final: 0.7383 (t70) outliers start: 10 outliers final: 7 residues processed: 128 average time/residue: 0.3382 time to fit residues: 63.2082 Evaluate side-chains 118 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 847 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 10 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.137559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112089 restraints weight = 15870.941| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.12 r_work: 0.3153 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11652 Z= 0.173 Angle : 0.546 7.154 15816 Z= 0.281 Chirality : 0.041 0.142 1832 Planarity : 0.004 0.035 1976 Dihedral : 8.206 75.458 1632 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.94 % Favored : 97.92 % Rotamer: Outliers : 1.61 % Allowed : 11.77 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.23), residues: 1440 helix: 2.23 (0.18), residues: 900 sheet: -4.24 (0.68), residues: 20 loop : -0.57 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 278 HIS 0.003 0.001 HIS A 615 PHE 0.031 0.001 PHE B 110 TYR 0.008 0.001 TYR A 76 ARG 0.003 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 676) hydrogen bonds : angle 3.76400 ( 1971) SS BOND : bond 0.00369 ( 6) SS BOND : angle 0.94816 ( 12) covalent geometry : bond 0.00420 (11646) covalent geometry : angle 0.54586 (15804) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 2.670 Fit side-chains REVERT: A 107 GLN cc_start: 0.7843 (mt0) cc_final: 0.7609 (mm-40) REVERT: A 308 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8675 (pp) REVERT: A 381 VAL cc_start: 0.8660 (t) cc_final: 0.8442 (t) REVERT: A 670 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7515 (tm-30) REVERT: B 75 ARG cc_start: 0.7883 (ttm170) cc_final: 0.7595 (ttp80) REVERT: B 113 VAL cc_start: 0.8496 (t) cc_final: 0.8190 (p) REVERT: B 308 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8688 (pp) REVERT: B 381 VAL cc_start: 0.8661 (t) cc_final: 0.8459 (t) REVERT: B 670 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7510 (tm-30) outliers start: 20 outliers final: 16 residues processed: 128 average time/residue: 0.4210 time to fit residues: 79.1347 Evaluate side-chains 122 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 847 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 444 ASN B 355 ASN B 444 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.140338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.115383 restraints weight = 15589.143| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.09 r_work: 0.3202 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11652 Z= 0.108 Angle : 0.484 7.985 15816 Z= 0.248 Chirality : 0.038 0.145 1832 Planarity : 0.004 0.034 1976 Dihedral : 7.631 73.704 1632 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.88 % Favored : 97.99 % Rotamer: Outliers : 1.69 % Allowed : 12.02 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.24), residues: 1440 helix: 2.49 (0.18), residues: 894 sheet: -4.30 (0.70), residues: 20 loop : -0.43 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 278 HIS 0.002 0.000 HIS B 579 PHE 0.010 0.001 PHE A 289 TYR 0.008 0.001 TYR B 76 ARG 0.003 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 676) hydrogen bonds : angle 3.58815 ( 1971) SS BOND : bond 0.00329 ( 6) SS BOND : angle 0.85564 ( 12) covalent geometry : bond 0.00245 (11646) covalent geometry : angle 0.48327 (15804) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 2.149 Fit side-chains REVERT: A 113 VAL cc_start: 0.8591 (t) cc_final: 0.8271 (p) REVERT: A 308 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8657 (pp) REVERT: A 332 MET cc_start: 0.6691 (tpt) cc_final: 0.6159 (tmm) REVERT: A 670 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7516 (tm-30) REVERT: B 75 ARG cc_start: 0.7778 (ttm170) cc_final: 0.7490 (ttp80) REVERT: B 113 VAL cc_start: 0.8388 (t) cc_final: 0.8097 (p) REVERT: B 308 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8667 (pp) REVERT: B 332 MET cc_start: 0.6710 (tpt) cc_final: 0.6150 (tmm) REVERT: B 670 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7534 (tm-30) outliers start: 21 outliers final: 13 residues processed: 132 average time/residue: 0.3817 time to fit residues: 74.7601 Evaluate side-chains 125 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 847 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 15 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 63 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 444 ASN A 630 HIS B 307 GLN B 355 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.137431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112042 restraints weight = 15926.299| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.12 r_work: 0.3152 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11652 Z= 0.154 Angle : 0.523 5.811 15816 Z= 0.270 Chirality : 0.040 0.144 1832 Planarity : 0.004 0.035 1976 Dihedral : 7.389 71.875 1632 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.85 % Allowed : 12.50 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.24), residues: 1440 helix: 2.33 (0.18), residues: 900 sheet: -4.22 (0.71), residues: 20 loop : -0.44 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 278 HIS 0.003 0.001 HIS B 615 PHE 0.018 0.001 PHE B 289 TYR 0.007 0.001 TYR B 76 ARG 0.002 0.000 ARG B 783 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 676) hydrogen bonds : angle 3.63138 ( 1971) SS BOND : bond 0.00368 ( 6) SS BOND : angle 0.86079 ( 12) covalent geometry : bond 0.00370 (11646) covalent geometry : angle 0.52271 (15804) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 1.338 Fit side-chains REVERT: A 308 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8636 (pp) REVERT: A 332 MET cc_start: 0.6705 (tpt) cc_final: 0.6102 (tmm) REVERT: A 670 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7537 (tm-30) REVERT: B 75 ARG cc_start: 0.7881 (ttm170) cc_final: 0.7604 (ttp80) REVERT: B 308 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8649 (pp) REVERT: B 332 MET cc_start: 0.6731 (tpt) cc_final: 0.6114 (tmm) REVERT: B 670 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7504 (tm-30) outliers start: 23 outliers final: 17 residues processed: 125 average time/residue: 0.2322 time to fit residues: 42.8725 Evaluate side-chains 125 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 847 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 78 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 120 optimal weight: 0.0570 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 0.0270 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116600 restraints weight = 15951.868| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.15 r_work: 0.3234 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11652 Z= 0.095 Angle : 0.460 5.698 15816 Z= 0.238 Chirality : 0.037 0.145 1832 Planarity : 0.003 0.034 1976 Dihedral : 6.566 69.841 1632 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.69 % Allowed : 13.31 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.24), residues: 1440 helix: 2.55 (0.18), residues: 894 sheet: -4.36 (0.72), residues: 20 loop : -0.31 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 278 HIS 0.002 0.000 HIS A 819 PHE 0.009 0.001 PHE A 110 TYR 0.008 0.001 TYR B 76 ARG 0.003 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 676) hydrogen bonds : angle 3.47605 ( 1971) SS BOND : bond 0.00335 ( 6) SS BOND : angle 0.78894 ( 12) covalent geometry : bond 0.00204 (11646) covalent geometry : angle 0.45989 (15804) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 2.672 Fit side-chains REVERT: A 308 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8615 (pp) REVERT: A 332 MET cc_start: 0.6671 (tpt) cc_final: 0.6126 (tmm) REVERT: A 381 VAL cc_start: 0.8542 (t) cc_final: 0.8334 (t) REVERT: A 670 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7517 (tm-30) REVERT: B 113 VAL cc_start: 0.8395 (t) cc_final: 0.8111 (p) REVERT: B 308 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8613 (pp) REVERT: B 332 MET cc_start: 0.6714 (tpt) cc_final: 0.6146 (tmm) REVERT: B 381 VAL cc_start: 0.8545 (t) cc_final: 0.8339 (t) REVERT: B 670 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7504 (tm-30) outliers start: 21 outliers final: 14 residues processed: 131 average time/residue: 0.3466 time to fit residues: 69.4067 Evaluate side-chains 124 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 594 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 65 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 57 optimal weight: 0.0270 overall best weight: 1.0840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.139798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114757 restraints weight = 15777.438| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.10 r_work: 0.3204 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11652 Z= 0.117 Angle : 0.484 5.759 15816 Z= 0.249 Chirality : 0.038 0.145 1832 Planarity : 0.004 0.048 1976 Dihedral : 6.350 68.743 1632 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.29 % Allowed : 13.71 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.24), residues: 1440 helix: 2.47 (0.18), residues: 900 sheet: -4.37 (0.71), residues: 20 loop : -0.35 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 278 HIS 0.002 0.001 HIS B 615 PHE 0.015 0.001 PHE B 110 TYR 0.007 0.001 TYR B 76 ARG 0.003 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 676) hydrogen bonds : angle 3.48871 ( 1971) SS BOND : bond 0.00314 ( 6) SS BOND : angle 0.81088 ( 12) covalent geometry : bond 0.00271 (11646) covalent geometry : angle 0.48416 (15804) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 1.306 Fit side-chains REVERT: A 308 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8586 (pp) REVERT: A 332 MET cc_start: 0.6709 (tpt) cc_final: 0.6154 (tmm) REVERT: A 670 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7520 (tm-30) REVERT: B 113 VAL cc_start: 0.8398 (t) cc_final: 0.8123 (p) REVERT: B 308 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8595 (pp) REVERT: B 332 MET cc_start: 0.6733 (tpt) cc_final: 0.6157 (tmm) REVERT: B 670 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7533 (tm-30) outliers start: 16 outliers final: 12 residues processed: 122 average time/residue: 0.3157 time to fit residues: 56.9102 Evaluate side-chains 124 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 663 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 23 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 115 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 97 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.141623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.116537 restraints weight = 15835.875| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.12 r_work: 0.3216 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11652 Z= 0.098 Angle : 0.464 5.715 15816 Z= 0.240 Chirality : 0.038 0.146 1832 Planarity : 0.004 0.048 1976 Dihedral : 5.939 65.218 1632 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.29 % Allowed : 13.63 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.23), residues: 1440 helix: 2.52 (0.18), residues: 902 sheet: -4.45 (0.69), residues: 20 loop : -0.31 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 278 HIS 0.002 0.000 HIS A 819 PHE 0.013 0.001 PHE B 110 TYR 0.007 0.001 TYR B 76 ARG 0.003 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 676) hydrogen bonds : angle 3.43744 ( 1971) SS BOND : bond 0.00308 ( 6) SS BOND : angle 0.77246 ( 12) covalent geometry : bond 0.00214 (11646) covalent geometry : angle 0.46344 (15804) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.315 Fit side-chains REVERT: A 308 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8507 (pp) REVERT: A 332 MET cc_start: 0.6616 (tpt) cc_final: 0.6111 (tmm) REVERT: A 670 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7491 (tm-30) REVERT: B 113 VAL cc_start: 0.8358 (t) cc_final: 0.8116 (p) REVERT: B 308 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8514 (pp) REVERT: B 332 MET cc_start: 0.6639 (tpt) cc_final: 0.6101 (tmm) REVERT: B 670 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7466 (tm-30) outliers start: 16 outliers final: 11 residues processed: 125 average time/residue: 0.2073 time to fit residues: 39.4012 Evaluate side-chains 125 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 663 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 122 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.135979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110570 restraints weight = 15880.531| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.11 r_work: 0.3143 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 11652 Z= 0.191 Angle : 0.567 7.779 15816 Z= 0.289 Chirality : 0.042 0.155 1832 Planarity : 0.004 0.050 1976 Dihedral : 6.413 69.244 1632 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.13 % Allowed : 13.95 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.23), residues: 1440 helix: 2.35 (0.18), residues: 900 sheet: -3.52 (0.84), residues: 24 loop : -0.36 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 303 HIS 0.003 0.001 HIS B 615 PHE 0.019 0.001 PHE A 289 TYR 0.009 0.001 TYR B 855 ARG 0.003 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 676) hydrogen bonds : angle 3.63184 ( 1971) SS BOND : bond 0.00409 ( 6) SS BOND : angle 0.86003 ( 12) covalent geometry : bond 0.00466 (11646) covalent geometry : angle 0.56622 (15804) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 1.177 Fit side-chains REVERT: A 308 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8623 (pp) REVERT: A 332 MET cc_start: 0.6804 (tpt) cc_final: 0.6183 (tmm) REVERT: B 308 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8630 (pp) REVERT: B 332 MET cc_start: 0.6743 (tpt) cc_final: 0.6140 (tmm) REVERT: B 670 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7533 (tm-30) REVERT: B 786 ASP cc_start: 0.7959 (t0) cc_final: 0.7590 (t70) outliers start: 14 outliers final: 12 residues processed: 122 average time/residue: 0.2388 time to fit residues: 42.6308 Evaluate side-chains 121 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 663 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 12 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.133215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108273 restraints weight = 15923.885| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.03 r_work: 0.3098 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 11652 Z= 0.235 Angle : 0.616 7.394 15816 Z= 0.316 Chirality : 0.044 0.177 1832 Planarity : 0.004 0.050 1976 Dihedral : 6.847 71.799 1632 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.53 % Allowed : 13.79 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.23), residues: 1440 helix: 2.05 (0.18), residues: 902 sheet: -3.41 (0.82), residues: 24 loop : -0.54 (0.30), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 303 HIS 0.003 0.001 HIS A 579 PHE 0.021 0.002 PHE A 289 TYR 0.009 0.001 TYR B 781 ARG 0.004 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.04646 ( 676) hydrogen bonds : angle 3.80831 ( 1971) SS BOND : bond 0.00451 ( 6) SS BOND : angle 0.93532 ( 12) covalent geometry : bond 0.00575 (11646) covalent geometry : angle 0.61564 (15804) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5956.02 seconds wall clock time: 112 minutes 2.56 seconds (6722.56 seconds total)