Starting phenix.real_space_refine on Sat Nov 16 15:17:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpr_36487/11_2024/8jpr_36487.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpr_36487/11_2024/8jpr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpr_36487/11_2024/8jpr_36487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpr_36487/11_2024/8jpr_36487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpr_36487/11_2024/8jpr_36487.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpr_36487/11_2024/8jpr_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-5513/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: 7.93, per 1000 atoms: 0.70 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: 3.00 Conformation dependent library (CDL) restraints added in 1.7 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: 1.28 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: 3.71 Time building geometry restraints manager: 3.39 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: 0.00 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: 1.340 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 30.220 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.050 ------------------------------------------------------------------------------- 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 11646 Z= 0.190 Angle : 0.556 8.080 15804 Z= 0.310 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 *********************** 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 : 1.305 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: 0.2903 time to fit residues: 97.8679 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 : 1.343 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 11646 Z= 0.353 Angle : 0.639 7.265 15804 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 *********************** 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 : 1.336 Fit side-chains REVERT: A 670 GLU cc_start: 0.7397 (tm-30) cc_final: 0.7127 (tm-30) REVERT: B 670 GLU cc_start: 0.7353 (tm-30) cc_final: 0.7133 (tm-30) outliers start: 16 outliers final: 11 residues processed: 143 average time/residue: 0.2498 time to fit residues: 51.4529 Evaluate side-chains 116 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 1.396 ------------------------------------------------------------------------------- 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 73 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 132 optimal weight: 0.0050 chunk 143 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 131 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11646 Z= 0.155 Angle : 0.502 8.942 15804 Z= 0.256 Chirality : 0.038 0.142 1832 Planarity : 0.004 0.033 1976 Dihedral : 8.297 82.700 1632 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.81 % Favored : 98.06 % Rotamer: Outliers : 0.81 % Allowed : 11.13 % Favored : 88.06 % 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: 1.77 (0.24), residues: 1440 helix: 2.31 (0.18), residues: 898 sheet: -4.32 (0.69), residues: 20 loop : -0.65 (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 327 PHE 0.009 0.001 PHE B 460 TYR 0.008 0.001 TYR A 76 ARG 0.003 0.000 ARG A 600 *********************** 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 135 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 1.422 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 132 average time/residue: 0.2626 time to fit residues: 49.3094 Evaluate side-chains 114 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 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 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 131 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS A 355 ASN ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 HIS B 355 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 11646 Z= 0.385 Angle : 0.623 7.108 15804 Z= 0.319 Chirality : 0.044 0.162 1832 Planarity : 0.004 0.038 1976 Dihedral : 8.382 74.802 1632 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.36 % Favored : 97.50 % Rotamer: Outliers : 1.61 % Allowed : 11.85 % Favored : 86.53 % 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: 1.52 (0.23), residues: 1440 helix: 2.04 (0.18), residues: 900 sheet: -4.23 (0.67), residues: 20 loop : -0.62 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 278 HIS 0.004 0.001 HIS A 615 PHE 0.031 0.002 PHE B 110 TYR 0.009 0.001 TYR B 781 ARG 0.003 0.001 ARG A 75 *********************** 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 130 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.233 Fit side-chains REVERT: A 381 VAL cc_start: 0.8263 (t) cc_final: 0.7993 (t) REVERT: B 381 VAL cc_start: 0.8256 (t) cc_final: 0.7997 (t) outliers start: 20 outliers final: 17 residues processed: 125 average time/residue: 0.2399 time to fit residues: 43.6397 Evaluate side-chains 118 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 1.394 ------------------------------------------------------------------------------- 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 389 VAL Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 551 ILE 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 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 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 117 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 HIS ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 11646 Z= 0.502 Angle : 0.690 8.055 15804 Z= 0.356 Chirality : 0.047 0.201 1832 Planarity : 0.005 0.045 1976 Dihedral : 8.554 74.012 1632 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.99 % Favored : 96.88 % Rotamer: Outliers : 2.02 % Allowed : 14.19 % Favored : 83.79 % 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: 1.10 (0.23), residues: 1440 helix: 1.65 (0.17), residues: 906 sheet: None (None), residues: 0 loop : -0.89 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 278 HIS 0.004 0.001 HIS A 455 PHE 0.022 0.002 PHE B 289 TYR 0.010 0.001 TYR A 781 ARG 0.004 0.001 ARG B 783 *********************** 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 137 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 1.702 Fit side-chains REVERT: A 126 LEU cc_start: 0.7002 (mt) cc_final: 0.6749 (pp) REVERT: A 381 VAL cc_start: 0.8317 (t) cc_final: 0.8046 (t) REVERT: B 381 VAL cc_start: 0.8319 (t) cc_final: 0.8040 (t) outliers start: 25 outliers final: 22 residues processed: 133 average time/residue: 0.2983 time to fit residues: 56.6546 Evaluate side-chains 125 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 1.716 ------------------------------------------------------------------------------- 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 174 ILE Chi-restraints excluded: chain A residue 188 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 587 LEU 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 150 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 587 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 47 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 27 optimal weight: 0.1980 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 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 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN A 742 HIS ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11646 Z= 0.164 Angle : 0.504 5.862 15804 Z= 0.261 Chirality : 0.039 0.144 1832 Planarity : 0.004 0.037 1976 Dihedral : 7.794 75.373 1632 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.53 % Allowed : 15.16 % Favored : 83.31 % 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 (0.24), residues: 1440 helix: 2.26 (0.18), residues: 896 sheet: -4.13 (0.74), residues: 20 loop : -0.62 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 278 HIS 0.002 0.000 HIS B 819 PHE 0.010 0.001 PHE A 289 TYR 0.009 0.001 TYR A 76 ARG 0.003 0.000 ARG B 364 *********************** 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 120 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.354 Fit side-chains REVERT: A 381 VAL cc_start: 0.8178 (t) cc_final: 0.7977 (t) REVERT: B 381 VAL cc_start: 0.8176 (t) cc_final: 0.7972 (t) outliers start: 19 outliers final: 14 residues processed: 114 average time/residue: 0.2588 time to fit residues: 42.8928 Evaluate side-chains 112 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 1.411 ------------------------------------------------------------------------------- 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 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 520 THR 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 136 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 140 optimal weight: 0.4980 chunk 88 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11646 Z= 0.209 Angle : 0.528 8.921 15804 Z= 0.269 Chirality : 0.039 0.144 1832 Planarity : 0.004 0.039 1976 Dihedral : 7.407 74.565 1632 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.45 % Allowed : 15.32 % Favored : 83.23 % 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: 1.83 (0.24), residues: 1440 helix: 2.33 (0.18), residues: 896 sheet: -4.26 (0.71), residues: 20 loop : -0.55 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 278 HIS 0.002 0.001 HIS A 819 PHE 0.015 0.001 PHE A 289 TYR 0.008 0.001 TYR A 76 ARG 0.003 0.000 ARG B 364 *********************** 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 125 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.341 Fit side-chains REVERT: A 126 LEU cc_start: 0.6888 (mt) cc_final: 0.6677 (pp) REVERT: A 381 VAL cc_start: 0.8152 (t) cc_final: 0.7932 (t) REVERT: B 381 VAL cc_start: 0.8149 (t) cc_final: 0.7928 (t) outliers start: 18 outliers final: 15 residues processed: 117 average time/residue: 0.2395 time to fit residues: 41.0616 Evaluate side-chains 117 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 436 ASN Chi-restraints excluded: chain A residue 520 THR 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 551 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 847 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 128 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: ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 11646 Z= 0.305 Angle : 0.565 6.581 15804 Z= 0.291 Chirality : 0.041 0.151 1832 Planarity : 0.004 0.038 1976 Dihedral : 7.301 73.153 1632 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.94 % Allowed : 14.92 % Favored : 83.15 % 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: 1.67 (0.23), residues: 1440 helix: 2.18 (0.18), residues: 900 sheet: -4.38 (0.68), residues: 20 loop : -0.59 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 278 HIS 0.003 0.001 HIS A 615 PHE 0.018 0.001 PHE A 289 TYR 0.008 0.001 TYR B 76 ARG 0.003 0.000 ARG B 364 *********************** 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 132 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: A 381 VAL cc_start: 0.8198 (t) cc_final: 0.7967 (t) REVERT: B 381 VAL cc_start: 0.8194 (t) cc_final: 0.7958 (t) outliers start: 24 outliers final: 22 residues processed: 121 average time/residue: 0.2554 time to fit residues: 44.9207 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 : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 125 CYS 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 436 ASN Chi-restraints excluded: chain A residue 520 THR 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 150 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 436 ASN 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 Chi-restraints excluded: chain B residue 847 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 40 optimal weight: 0.0670 chunk 118 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- 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 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11646 Z= 0.207 Angle : 0.515 5.974 15804 Z= 0.266 Chirality : 0.039 0.146 1832 Planarity : 0.004 0.038 1976 Dihedral : 6.830 72.174 1632 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.69 % Allowed : 15.48 % Favored : 82.82 % 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: 1.80 (0.23), residues: 1440 helix: 2.29 (0.18), residues: 896 sheet: -4.32 (0.73), residues: 20 loop : -0.52 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 278 HIS 0.002 0.001 HIS B 819 PHE 0.014 0.001 PHE A 289 TYR 0.008 0.001 TYR A 76 ARG 0.004 0.000 ARG B 364 *********************** 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: 21 poor density : 105 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: A 381 VAL cc_start: 0.8136 (t) cc_final: 0.7911 (t) REVERT: B 381 VAL cc_start: 0.8141 (t) cc_final: 0.7914 (t) outliers start: 21 outliers final: 19 residues processed: 118 average time/residue: 0.2350 time to fit residues: 41.3278 Evaluate side-chains 123 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 436 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 587 LEU 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 125 CYS 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 520 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 1.9990 chunk 84 optimal weight: 0.0370 chunk 65 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.003 0.025 11646 Z= 0.205 Angle : 0.515 5.834 15804 Z= 0.266 Chirality : 0.039 0.146 1832 Planarity : 0.004 0.039 1976 Dihedral : 6.457 70.535 1632 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.77 % Allowed : 15.32 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.84 (0.23), residues: 1440 helix: 2.34 (0.18), residues: 896 sheet: -4.25 (0.74), residues: 20 loop : -0.55 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 278 HIS 0.002 0.001 HIS B 819 PHE 0.014 0.001 PHE B 110 TYR 0.008 0.001 TYR B 76 ARG 0.003 0.000 ARG B 364 ********************** 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 127 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 1.328 Fit side-chains revert: symmetry clash REVERT: A 381 VAL cc_start: 0.8114 (t) cc_final: 0.7879 (t) REVERT: B 381 VAL cc_start: 0.8115 (t) cc_final: 0.7882 (t) outliers start: 22 outliers final: 21 residues processed: 119 average time/residue: 0.2328 time to fit residues: 41.4338 Evaluate side-chains 126 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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 436 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 587 LEU 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 125 CYS 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 520 THR Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 587 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 17 optimal weight: 0.0270 chunk 32 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- 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 ** 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 = 0.136023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111850 restraints weight = 15616.848| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.05 r_work: 0.3171 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11646 Z= 0.188 Angle : 0.508 5.862 15804 Z= 0.262 Chirality : 0.039 0.146 1832 Planarity : 0.004 0.039 1976 Dihedral : 6.151 68.824 1632 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.61 % Allowed : 15.56 % Favored : 82.82 % 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: 1.91 (0.23), residues: 1440 helix: 2.39 (0.18), residues: 896 sheet: -4.22 (0.75), residues: 20 loop : -0.52 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 278 HIS 0.002 0.001 HIS A 327 PHE 0.013 0.001 PHE B 110 TYR 0.008 0.001 TYR B 76 ARG 0.003 0.000 ARG B 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.30 seconds wall clock time: 42 minutes 44.76 seconds (2564.76 seconds total)