Starting phenix.real_space_refine on Fri Jul 3 01:23:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jpr_36487/07_2026/8jpr_36487.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpr_36487/07_2026/8jpr_36487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jpr_36487/07_2026/8jpr_36487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpr_36487/07_2026/8jpr_36487.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8jpr_36487/07_2026/8jpr_36487.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jpr_36487/07_2026/8jpr_36487.cif" model { file = "/net/cci-nas-00/data/ceres_data/8jpr_36487/07_2026/8jpr_36487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpr_36487/07_2026/8jpr_36487.cif" } 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-dev-6108/lib/python3.11/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: 2.85, per 1000 atoms: 0.25 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: 0.96 Conformation dependent library (CDL) restraints added in 544.9 milliseconds 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: 0.33 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: 1.82 Time building geometry restraints manager: 1.27 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 - 14.94: 6109 14.94 - 29.87: 556 29.87 - 44.81: 145 44.81 - 59.74: 20 59.74 - 74.68: 10 Dihedral angle restraints: 6840 sinusoidal: 2664 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 6837 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.350 Find NCS groups from input model: 0.310 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: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 14.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 12.453 74.677 4138 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 are 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/Z covalent geometry : bond 0.00283 / 0.13 (11646) covalent geometry : angle 0.55633 / 0.31 (15804) SS BOND : bond 0.00528 / 0.26 ( 6) SS BOND : angle 2.17950 / 1.20 ( 12) hydrogen bonds : bond 0.14621 / 10.18 ( 676) hydrogen bonds : angle 6.31140 / 4.68 ( 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 : 0.415 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: 0.1173 time to fit residues: 40.1554 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 : 0.318 ------------------------------------------------------------------------------- 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... 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 = 0.133627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.108658 restraints weight = 16015.842| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.07 r_work: 0.3133 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2529 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= 0.247 Angle : 0.666 7.198 15816 Z= 0.343 Chirality : 0.045 0.166 1832 Planarity : 0.005 0.041 1976 Dihedral : 4.560 21.457 1570 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.45 % Allowed : 8.95 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.23), residues: 1440 helix: 1.66 (0.18), residues: 898 sheet: -4.28 (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 0.020 0.002 PHE B 473 TRP 0.010 0.001 TRP B 303 HIS 0.005 0.001 HIS A 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.25 (11646) covalent geometry : angle 0.66545 / 0.34 (15804) SS BOND : bond 0.00554 / 0.25 ( 6) SS BOND : angle 1.19970 / 0.66 ( 12) hydrogen bonds : bond 0.04912 / 3.28 ( 676) hydrogen bonds : angle 4.14513 / 3.02 ( 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 149 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.445 Fit side-chains REVERT: A 670 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7508 (tm-30) REVERT: A 732 MET cc_start: 0.6000 (tmm) cc_final: 0.5793 (tmm) REVERT: A 786 ASP cc_start: 0.7856 (t0) cc_final: 0.7432 (t70) REVERT: B 670 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7477 (tm-30) REVERT: B 786 ASP cc_start: 0.7818 (t0) cc_final: 0.7392 (t70) outliers start: 18 outliers final: 11 residues processed: 144 average time/residue: 0.0994 time to fit residues: 21.1414 Evaluate side-chains 119 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 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: 3.9990 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: 2.9990 chunk 78 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 67 optimal weight: 0.3980 chunk 42 optimal weight: 0.7980 chunk 100 optimal weight: 0.0980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 444 ASN B 444 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.140122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.115269 restraints weight = 15686.065| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.12 r_work: 0.3222 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11652 Z= 0.104 Angle : 0.503 8.306 15816 Z= 0.256 Chirality : 0.038 0.142 1832 Planarity : 0.004 0.034 1976 Dihedral : 4.111 17.112 1570 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.81 % Favored : 98.06 % Rotamer: Outliers : 0.89 % Allowed : 11.37 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.24), residues: 1440 helix: 2.25 (0.18), residues: 898 sheet: -4.29 (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 B 400 TYR 0.008 0.001 TYR A 76 PHE 0.015 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/Z covalent geometry : bond 0.00225 / 0.10 (11646) covalent geometry : angle 0.50221 / 0.26 (15804) SS BOND : bond 0.00329 / 0.14 ( 6) SS BOND : angle 0.87566 / 0.43 ( 12) hydrogen bonds : bond 0.03682 / 2.48 ( 676) hydrogen bonds : angle 3.72599 / 2.76 ( 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 136 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8705 (pp) REVERT: A 332 MET cc_start: 0.6682 (tpt) cc_final: 0.6289 (mpp) REVERT: A 670 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7471 (tm-30) REVERT: B 308 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8714 (pp) REVERT: B 332 MET cc_start: 0.6671 (tpt) cc_final: 0.6274 (mpp) REVERT: B 670 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7467 (tm-30) REVERT: B 734 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7840 (tp30) REVERT: B 786 ASP cc_start: 0.7795 (t0) cc_final: 0.7361 (t70) outliers start: 11 outliers final: 7 residues processed: 133 average time/residue: 0.1079 time to fit residues: 20.9472 Evaluate side-chains 120 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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: 0.8980 chunk 110 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 140 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.135395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110736 restraints weight = 15842.491| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.06 r_work: 0.3154 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11652 Z= 0.173 Angle : 0.552 7.277 15816 Z= 0.281 Chirality : 0.041 0.142 1832 Planarity : 0.004 0.035 1976 Dihedral : 4.172 20.705 1570 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.81 % Favored : 98.06 % Rotamer: Outliers : 1.85 % Allowed : 11.21 % 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 are not related in a simple way. whole: 1.71 (0.23), residues: 1440 helix: 2.22 (0.18), residues: 898 sheet: -4.18 (0.69), residues: 20 loop : -0.59 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 364 TYR 0.007 0.001 TYR A 781 PHE 0.025 0.001 PHE B 110 TRP 0.010 0.001 TRP B 278 HIS 0.003 0.001 HIS B 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 (11646) covalent geometry : angle 0.55120 / 0.28 (15804) SS BOND : bond 0.00357 / 0.16 ( 6) SS BOND : angle 0.94244 / 0.45 ( 12) hydrogen bonds : bond 0.04215 / 2.82 ( 676) hydrogen bonds : angle 3.77576 / 2.78 ( 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 137 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 GLN cc_start: 0.7810 (mt0) cc_final: 0.7598 (mm-40) REVERT: A 308 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8720 (pp) REVERT: A 670 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7519 (tm-30) REVERT: B 113 VAL cc_start: 0.8507 (t) cc_final: 0.8212 (p) REVERT: B 308 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8683 (pp) REVERT: B 670 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7513 (tm-30) outliers start: 23 outliers final: 18 residues processed: 132 average time/residue: 0.1068 time to fit residues: 20.6871 Evaluate side-chains 124 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 389 VAL Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 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 25 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN A 444 ASN B 444 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.138047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.113545 restraints weight = 15580.005| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.07 r_work: 0.3195 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2976 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= 0.113 Angle : 0.487 5.853 15816 Z= 0.250 Chirality : 0.038 0.144 1832 Planarity : 0.004 0.034 1976 Dihedral : 3.988 17.764 1570 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.94 % Favored : 97.92 % Rotamer: Outliers : 1.77 % Allowed : 11.85 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.24), residues: 1440 helix: 2.41 (0.18), residues: 894 sheet: -4.18 (0.73), residues: 20 loop : -0.41 (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 B 76 PHE 0.013 0.001 PHE A 351 TRP 0.011 0.001 TRP B 278 HIS 0.002 0.000 HIS B 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (11646) covalent geometry : angle 0.48637 / 0.25 (15804) SS BOND : bond 0.00315 / 0.14 ( 6) SS BOND : angle 0.88741 / 0.42 ( 12) hydrogen bonds : bond 0.03655 / 2.46 ( 676) hydrogen bonds : angle 3.61193 / 2.68 ( 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 138 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 308 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8695 (pp) REVERT: A 332 MET cc_start: 0.6613 (tpt) cc_final: 0.6097 (tmm) REVERT: A 670 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7512 (tm-30) REVERT: B 308 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8653 (pp) REVERT: B 332 MET cc_start: 0.6728 (tpt) cc_final: 0.6155 (tmm) REVERT: B 670 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7533 (tm-30) REVERT: B 734 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7820 (tp30) outliers start: 22 outliers final: 14 residues processed: 132 average time/residue: 0.0902 time to fit residues: 17.9366 Evaluate side-chains 122 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 73.4512 > 50: distance: 55 - 61: 33.942 distance: 61 - 62: 15.912 distance: 62 - 63: 58.194 distance: 63 - 64: 43.052 distance: 63 - 65: 40.347 distance: 65 - 66: 8.712 distance: 66 - 67: 50.578 distance: 66 - 69: 42.946 distance: 67 - 72: 57.039 distance: 69 - 70: 12.453 distance: 69 - 71: 29.439 distance: 74 - 83: 39.544 distance: 76 - 77: 47.998 distance: 77 - 78: 15.371 distance: 77 - 79: 13.695 distance: 83 - 84: 15.121 distance: 84 - 85: 46.488 distance: 84 - 87: 62.601 distance: 85 - 86: 40.997 distance: 85 - 89: 68.688 distance: 86 - 110: 38.490 distance: 87 - 88: 38.772 distance: 89 - 90: 55.942 distance: 89 - 95: 58.036 distance: 91 - 92: 27.169 distance: 92 - 118: 44.906 distance: 96 - 97: 36.959 distance: 97 - 98: 34.606 distance: 97 - 100: 36.022 distance: 98 - 99: 41.146 distance: 98 - 103: 56.458 distance: 99 - 123: 40.375 distance: 100 - 101: 40.422 distance: 100 - 102: 38.663 distance: 103 - 104: 38.694 distance: 104 - 105: 39.934 distance: 104 - 107: 57.498 distance: 105 - 106: 55.977 distance: 105 - 110: 41.222 distance: 106 - 131: 33.922 distance: 107 - 108: 31.691 distance: 107 - 109: 55.149 distance: 110 - 111: 56.467 distance: 111 - 112: 47.960 distance: 111 - 114: 38.791 distance: 112 - 113: 41.502 distance: 112 - 118: 47.995 distance: 113 - 138: 28.786 distance: 114 - 115: 39.019 distance: 115 - 116: 27.523 distance: 115 - 117: 39.336 distance: 119 - 122: 56.775 distance: 120 - 121: 40.111 distance: 121 - 145: 31.607 distance: 123 - 124: 23.126 distance: 124 - 125: 28.529 distance: 124 - 127: 60.124 distance: 125 - 126: 49.436 distance: 125 - 131: 21.463 distance: 126 - 151: 36.679 distance: 127 - 128: 39.385 distance: 128 - 129: 56.203 distance: 128 - 130: 39.316