Starting phenix.real_space_refine on Sat Aug 23 10:07:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jpr_36487/08_2025/8jpr_36487.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpr_36487/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jpr_36487/08_2025/8jpr_36487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpr_36487/08_2025/8jpr_36487.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jpr_36487/08_2025/8jpr_36487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpr_36487/08_2025/8jpr_36487.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.058 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'GLU:plan': 4, 'TYR:plan': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'ARG: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: {'GLU:plan': 4, 'TYR:plan': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'ARG: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: 3.02, per 1000 atoms: 0.27 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: 1.00 Conformation dependent library (CDL) restraints added in 555.0 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.40 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: 2.00 Time building geometry restraints manager: 1.32 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: 0.02 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.320 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.190 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.004 0.000 ARG B 501 TYR 0.007 0.001 TYR A 781 PHE 0.023 0.001 PHE B 101 TRP 0.010 0.001 TRP B 278 HIS 0.002 0.001 HIS A 834 Details of bonding type rmsd covalent geometry : bond 0.00283 (11646) covalent geometry : angle 0.55633 (15804) SS BOND : bond 0.00528 ( 6) SS BOND : angle 2.17950 ( 12) hydrogen bonds : bond 0.14621 ( 676) hydrogen bonds : angle 6.31140 ( 1971) *********************** 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 : 0.462 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: 0.1379 time to fit residues: 46.7740 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 : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.133651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.108723 restraints weight = 16009.507| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.06 r_work: 0.3133 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 11652 Z= 0.246 Angle : 0.666 7.154 15816 Z= 0.344 Chirality : 0.045 0.164 1832 Planarity : 0.005 0.041 1976 Dihedral : 8.922 85.623 1632 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.45 % Allowed : 8.87 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.23), residues: 1440 helix: 1.67 (0.18), residues: 898 sheet: -4.27 (0.61), residues: 20 loop : -0.83 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 295 TYR 0.011 0.001 TYR B 806 PHE 0.019 0.002 PHE B 473 TRP 0.009 0.001 TRP B 278 HIS 0.005 0.001 HIS A 455 Details of bonding type rmsd covalent geometry : bond 0.00602 (11646) covalent geometry : angle 0.66521 (15804) SS BOND : bond 0.00561 ( 6) SS BOND : angle 1.20074 ( 12) hydrogen bonds : bond 0.04907 ( 676) hydrogen bonds : angle 4.14312 ( 1971) *********************** 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: 18 poor density : 130 time to evaluate : 0.464 Fit side-chains REVERT: A 670 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7523 (tm-30) REVERT: A 732 MET cc_start: 0.6024 (tmm) cc_final: 0.5818 (tmm) REVERT: A 786 ASP cc_start: 0.7865 (t0) cc_final: 0.7454 (t70) REVERT: B 670 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7509 (tm-30) REVERT: B 786 ASP cc_start: 0.7846 (t0) cc_final: 0.7433 (t70) outliers start: 18 outliers final: 12 residues processed: 143 average time/residue: 0.1066 time to fit residues: 22.4641 Evaluate side-chains 120 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 150 ILE 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 150 ILE Chi-restraints excluded: chain B residue 188 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 121 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 113 optimal weight: 0.4980 chunk 109 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 67 optimal weight: 0.0570 chunk 42 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 overall best weight: 0.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.142146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116546 restraints weight = 15740.269| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.14 r_work: 0.3216 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11652 Z= 0.106 Angle : 0.503 7.324 15816 Z= 0.257 Chirality : 0.038 0.142 1832 Planarity : 0.004 0.033 1976 Dihedral : 8.318 81.675 1632 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.81 % Favored : 98.06 % Rotamer: Outliers : 0.81 % Allowed : 11.29 % Favored : 87.90 % 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 aren not related in a simple way. whole: 1.70 (0.23), residues: 1440 helix: 2.25 (0.18), residues: 898 sheet: -4.30 (0.69), residues: 20 loop : -0.68 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 364 TYR 0.008 0.001 TYR A 76 PHE 0.014 0.001 PHE A 351 TRP 0.011 0.001 TRP B 278 HIS 0.001 0.000 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00229 (11646) covalent geometry : angle 0.50250 (15804) SS BOND : bond 0.00360 ( 6) SS BOND : angle 0.86354 ( 12) hydrogen bonds : bond 0.03678 ( 676) hydrogen bonds : angle 3.71814 ( 1971) *********************** 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 134 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.439 Fit side-chains REVERT: A 308 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8707 (pp) REVERT: A 332 MET cc_start: 0.6685 (tpt) cc_final: 0.6276 (mpp) REVERT: A 670 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7480 (tm-30) REVERT: B 308 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8704 (pp) REVERT: B 332 MET cc_start: 0.6693 (tpt) cc_final: 0.6275 (mpp) REVERT: B 670 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7479 (tm-30) REVERT: B 734 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7812 (tp30) outliers start: 10 outliers final: 7 residues processed: 131 average time/residue: 0.1135 time to fit residues: 21.4220 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 : 0.356 ------------------------------------------------------------------------------- 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 14 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 65 optimal weight: 0.0970 chunk 140 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 327 HIS ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 HIS ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.138609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114011 restraints weight = 15788.673| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.09 r_work: 0.3203 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11652 Z= 0.124 Angle : 0.501 7.269 15816 Z= 0.257 Chirality : 0.039 0.143 1832 Planarity : 0.004 0.033 1976 Dihedral : 8.016 75.709 1632 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.53 % Favored : 98.33 % Rotamer: Outliers : 1.37 % Allowed : 11.69 % Favored : 86.94 % 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 aren not related in a simple way. whole: 1.89 (0.24), residues: 1440 helix: 2.36 (0.18), residues: 898 sheet: -4.19 (0.73), residues: 20 loop : -0.52 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 364 TYR 0.008 0.001 TYR B 76 PHE 0.028 0.001 PHE B 110 TRP 0.010 0.001 TRP B 278 HIS 0.002 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00288 (11646) covalent geometry : angle 0.50041 (15804) SS BOND : bond 0.00350 ( 6) SS BOND : angle 0.87405 ( 12) hydrogen bonds : bond 0.03743 ( 676) hydrogen bonds : angle 3.67098 ( 1971) *********************** 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: 17 poor density : 116 time to evaluate : 0.429 Fit side-chains REVERT: A 107 GLN cc_start: 0.7810 (mt0) cc_final: 0.7588 (mm-40) REVERT: A 308 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8680 (pp) REVERT: A 332 MET cc_start: 0.6732 (tpt) cc_final: 0.6325 (mpp) REVERT: A 670 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7482 (tm-30) REVERT: B 308 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8691 (pp) REVERT: B 332 MET cc_start: 0.6723 (tpt) cc_final: 0.6293 (mpp) REVERT: B 670 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7479 (tm-30) outliers start: 17 outliers final: 11 residues processed: 127 average time/residue: 0.1121 time to fit residues: 20.7349 Evaluate side-chains 116 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 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 847 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 25 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 123 optimal weight: 0.0370 chunk 55 optimal weight: 0.0980 chunk 134 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 overall best weight: 2.2264 ------------------------------------------------------------------------------- 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** A 630 HIS B 355 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.134362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109796 restraints weight = 15760.115| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.06 r_work: 0.3141 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3061 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= 0.187 Angle : 0.562 7.918 15816 Z= 0.287 Chirality : 0.041 0.145 1832 Planarity : 0.004 0.035 1976 Dihedral : 7.913 73.262 1632 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.15 % Favored : 97.71 % Rotamer: Outliers : 2.10 % Allowed : 11.77 % Favored : 86.13 % 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 aren not related in a simple way. whole: 1.73 (0.23), residues: 1440 helix: 2.21 (0.18), residues: 900 sheet: -4.17 (0.69), residues: 20 loop : -0.54 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 364 TYR 0.008 0.001 TYR A 781 PHE 0.018 0.001 PHE A 289 TRP 0.009 0.001 TRP B 278 HIS 0.003 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00457 (11646) covalent geometry : angle 0.56128 (15804) SS BOND : bond 0.00408 ( 6) SS BOND : angle 0.92067 ( 12) hydrogen bonds : bond 0.04268 ( 676) hydrogen bonds : angle 3.74077 ( 1971) *********************** 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 135 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.581 Fit side-chains REVERT: A 308 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8720 (pp) REVERT: A 332 MET cc_start: 0.6770 (tpt) cc_final: 0.6196 (tmm) REVERT: A 670 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7512 (tm-30) REVERT: B 308 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8719 (pp) REVERT: B 332 MET cc_start: 0.6790 (tpt) cc_final: 0.6209 (tmm) REVERT: B 670 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7508 (tm-30) outliers start: 26 outliers final: 21 residues processed: 128 average time/residue: 0.1112 time to fit residues: 20.8966 Evaluate side-chains 121 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 113 VAL 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 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 113 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 70 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 113 optimal weight: 0.0980 chunk 132 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 88 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.139076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.113918 restraints weight = 15798.419| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.11 r_work: 0.3179 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11652 Z= 0.121 Angle : 0.490 5.758 15816 Z= 0.252 Chirality : 0.039 0.145 1832 Planarity : 0.004 0.035 1976 Dihedral : 7.348 73.156 1632 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.77 % Allowed : 12.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.24), residues: 1440 helix: 2.41 (0.18), residues: 896 sheet: -4.16 (0.73), residues: 20 loop : -0.44 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 364 TYR 0.008 0.001 TYR A 76 PHE 0.015 0.001 PHE A 351 TRP 0.011 0.001 TRP A 278 HIS 0.002 0.001 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00281 (11646) covalent geometry : angle 0.48945 (15804) SS BOND : bond 0.00331 ( 6) SS BOND : angle 0.85793 ( 12) hydrogen bonds : bond 0.03702 ( 676) hydrogen bonds : angle 3.59192 ( 1971) *********************** 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 128 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.441 Fit side-chains REVERT: A 308 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8695 (pp) REVERT: A 332 MET cc_start: 0.6655 (tpt) cc_final: 0.6097 (tmm) REVERT: A 670 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7535 (tm-30) REVERT: B 308 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8690 (pp) REVERT: B 332 MET cc_start: 0.6719 (tpt) cc_final: 0.6169 (tmm) REVERT: B 670 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7523 (tm-30) outliers start: 22 outliers final: 16 residues processed: 120 average time/residue: 0.1092 time to fit residues: 19.4092 Evaluate side-chains 118 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 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 551 ILE Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 790 LEU 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 389 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 144 optimal weight: 0.5980 chunk 99 optimal weight: 0.0980 chunk 132 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 127 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.142495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.117169 restraints weight = 15694.377| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.13 r_work: 0.3225 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3263 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= 0.096 Angle : 0.461 5.697 15816 Z= 0.238 Chirality : 0.037 0.145 1832 Planarity : 0.003 0.034 1976 Dihedral : 6.363 69.122 1632 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.61 % Allowed : 12.98 % Favored : 85.40 % 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 aren not related in a simple way. whole: 2.19 (0.24), residues: 1440 helix: 2.57 (0.18), residues: 894 sheet: -4.28 (0.73), residues: 20 loop : -0.30 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 364 TYR 0.007 0.001 TYR A 76 PHE 0.014 0.001 PHE A 351 TRP 0.011 0.001 TRP A 278 HIS 0.002 0.000 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00205 (11646) covalent geometry : angle 0.46041 (15804) SS BOND : bond 0.00317 ( 6) SS BOND : angle 0.77320 ( 12) hydrogen bonds : bond 0.03263 ( 676) hydrogen bonds : angle 3.47690 ( 1971) *********************** 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 140 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.433 Fit side-chains REVERT: A 308 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8615 (pp) REVERT: A 332 MET cc_start: 0.6660 (tpt) cc_final: 0.6124 (tmm) REVERT: A 670 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7441 (tm-30) REVERT: B 308 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8628 (pp) REVERT: B 332 MET cc_start: 0.6650 (tpt) cc_final: 0.6117 (tmm) REVERT: B 670 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7434 (tm-30) outliers start: 20 outliers final: 14 residues processed: 132 average time/residue: 0.0999 time to fit residues: 19.9910 Evaluate side-chains 123 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 444 ASN Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 815 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 84 optimal weight: 0.4980 chunk 140 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.139770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114629 restraints weight = 15733.908| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.11 r_work: 0.3189 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11652 Z= 0.127 Angle : 0.494 7.180 15816 Z= 0.253 Chirality : 0.039 0.145 1832 Planarity : 0.004 0.048 1976 Dihedral : 6.275 68.395 1632 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.45 % Allowed : 13.23 % Favored : 85.32 % 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 aren not related in a simple way. whole: 2.15 (0.24), residues: 1440 helix: 2.53 (0.18), residues: 898 sheet: -4.22 (0.75), residues: 20 loop : -0.31 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 364 TYR 0.007 0.001 TYR A 76 PHE 0.015 0.001 PHE B 289 TRP 0.009 0.001 TRP B 278 HIS 0.002 0.001 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00297 (11646) covalent geometry : angle 0.49401 (15804) SS BOND : bond 0.00318 ( 6) SS BOND : angle 0.78333 ( 12) hydrogen bonds : bond 0.03553 ( 676) hydrogen bonds : angle 3.48687 ( 1971) *********************** 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 127 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.458 Fit side-chains REVERT: A 308 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8615 (pp) REVERT: A 332 MET cc_start: 0.6712 (tpt) cc_final: 0.6170 (tmm) REVERT: A 670 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7470 (tm-30) REVERT: B 308 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8636 (pp) REVERT: B 332 MET cc_start: 0.6681 (tpt) cc_final: 0.6145 (tmm) outliers start: 18 outliers final: 15 residues processed: 122 average time/residue: 0.1020 time to fit residues: 18.6665 Evaluate side-chains 123 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 389 VAL 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 A residue 815 SER 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 12 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 115 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 444 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 = 0.3637 r_free = 0.3637 target = 0.139481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.115250 restraints weight = 15525.728| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.07 r_work: 0.3214 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3367 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= 0.101 Angle : 0.471 5.894 15816 Z= 0.241 Chirality : 0.038 0.146 1832 Planarity : 0.004 0.047 1976 Dihedral : 5.951 65.998 1632 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.24), residues: 1440 helix: 2.58 (0.18), residues: 900 sheet: -4.31 (0.73), residues: 20 loop : -0.27 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 364 TYR 0.007 0.001 TYR A 76 PHE 0.013 0.001 PHE A 351 TRP 0.011 0.001 TRP B 278 HIS 0.002 0.000 HIS B 819 Details of bonding type rmsd covalent geometry : bond 0.00224 (11646) covalent geometry : angle 0.47035 (15804) SS BOND : bond 0.00291 ( 6) SS BOND : angle 0.73842 ( 12) hydrogen bonds : bond 0.03323 ( 676) hydrogen bonds : angle 3.43323 ( 1971) *********************** 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 126 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.460 Fit side-chains REVERT: A 308 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8625 (pp) REVERT: A 332 MET cc_start: 0.6656 (tpt) cc_final: 0.6146 (tmm) REVERT: A 670 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7477 (tm-30) REVERT: B 308 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8630 (pp) REVERT: B 332 MET cc_start: 0.6639 (tpt) cc_final: 0.6119 (tmm) outliers start: 16 outliers final: 13 residues processed: 120 average time/residue: 0.1080 time to fit residues: 19.5806 Evaluate side-chains 123 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 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 551 ILE Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 815 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 126 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 62 optimal weight: 0.0470 chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- 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** ** B 444 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 = 0.3595 r_free = 0.3595 target = 0.136105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111231 restraints weight = 15742.387| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.07 r_work: 0.3137 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 11652 Z= 0.185 Angle : 0.553 5.926 15816 Z= 0.283 Chirality : 0.042 0.149 1832 Planarity : 0.004 0.050 1976 Dihedral : 6.379 69.599 1632 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.45 % Allowed : 13.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.23), residues: 1440 helix: 2.39 (0.18), residues: 900 sheet: -3.38 (0.87), residues: 24 loop : -0.37 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 364 TYR 0.007 0.001 TYR B 781 PHE 0.019 0.001 PHE A 289 TRP 0.008 0.001 TRP A 303 HIS 0.003 0.001 HIS B 819 Details of bonding type rmsd covalent geometry : bond 0.00453 (11646) covalent geometry : angle 0.55236 (15804) SS BOND : bond 0.00360 ( 6) SS BOND : angle 0.83937 ( 12) hydrogen bonds : bond 0.04120 ( 676) hydrogen bonds : angle 3.60477 ( 1971) ********************** 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 125 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.296 Fit side-chains REVERT: A 308 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8644 (pp) REVERT: A 332 MET cc_start: 0.6762 (tpt) cc_final: 0.6177 (tmm) REVERT: A 670 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7550 (tm-30) REVERT: B 308 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8659 (pp) REVERT: B 332 MET cc_start: 0.6744 (tpt) cc_final: 0.6159 (tmm) REVERT: B 786 ASP cc_start: 0.7969 (t0) cc_final: 0.7608 (t70) outliers start: 18 outliers final: 16 residues processed: 122 average time/residue: 0.0946 time to fit residues: 16.8865 Evaluate side-chains 124 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 663 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 815 SER 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 389 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 815 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 5 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 67 optimal weight: 0.4980 chunk 134 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 444 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 = 0.3600 r_free = 0.3600 target = 0.136530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111438 restraints weight = 15874.614| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.10 r_work: 0.3152 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3483 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= 0.161 Angle : 0.531 5.838 15816 Z= 0.272 Chirality : 0.040 0.145 1832 Planarity : 0.004 0.050 1976 Dihedral : 6.294 69.337 1632 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.61 % Allowed : 13.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.23), residues: 1440 helix: 2.36 (0.18), residues: 900 sheet: -3.40 (0.86), residues: 24 loop : -0.41 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 364 TYR 0.008 0.001 TYR B 76 PHE 0.017 0.001 PHE B 289 TRP 0.009 0.001 TRP B 278 HIS 0.003 0.001 HIS A 579 Details of bonding type rmsd covalent geometry : bond 0.00391 (11646) covalent geometry : angle 0.53064 (15804) SS BOND : bond 0.00349 ( 6) SS BOND : angle 0.84895 ( 12) hydrogen bonds : bond 0.03964 ( 676) hydrogen bonds : angle 3.59652 ( 1971) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2695.83 seconds wall clock time: 47 minutes 6.97 seconds (2826.97 seconds total)