Starting phenix.real_space_refine on Sat Aug 23 03:26:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bog_44735/08_2025/9bog_44735.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bog_44735/08_2025/9bog_44735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bog_44735/08_2025/9bog_44735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bog_44735/08_2025/9bog_44735.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bog_44735/08_2025/9bog_44735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bog_44735/08_2025/9bog_44735.map" } resolution = 3.99 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= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 5838 2.51 5 N 1705 2.21 5 O 1807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9370 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 5496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 5496 Classifications: {'peptide': 800} Incomplete info: {'truncation_to_alanine': 204} Link IDs: {'PTRANS': 31, 'TRANS': 768} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 714 Unresolved non-hydrogen angles: 913 Unresolved non-hydrogen dihedrals: 575 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'ASP:plan': 24, 'ARG:plan': 15, 'GLU:plan': 16, 'GLN:plan1': 16, 'TYR:plan': 8, 'ASN:plan1': 18, 'PHE:plan': 2, 'HIS:plan': 5, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 439 Chain: "F" Number of atoms: 884 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 154, 884 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 145} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 12, 'PHE:plan': 4, 'ASP:plan': 2, 'GLN:plan1': 6, 'ARG:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 140 Chain: "C" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1356 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 14, 'TRANS': 190} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 7, 'GLU:plan': 7, 'ASN:plan1': 8, 'GLN:plan1': 2, 'ARG:plan': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "H" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 1634 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 262} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 448 Unresolved non-hydrogen angles: 595 Unresolved non-hydrogen dihedrals: 369 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'PHE:plan': 6, 'ASN:plan1': 15, 'TYR:plan': 10, 'GLN:plan1': 7, 'HIS:plan': 1, 'ASP:plan': 7, 'GLU:plan': 2, 'ARG:plan': 4, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 251 Time building chain proxies: 2.06, per 1000 atoms: 0.22 Number of scatterers: 9370 At special positions: 0 Unit cell: (81.6, 92.4, 163.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1807 8.00 N 1705 7.00 C 5838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 810 " - pdb=" SG CYS D 832 " distance=2.04 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 56 " distance=2.03 Simple disulfide: pdb=" SG CYS H 3 " - pdb=" SG CYS H 44 " distance=2.03 Simple disulfide: pdb=" SG CYS H 161 " - pdb=" SG CYS H 187 " 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: 0.77 Conformation dependent library (CDL) restraints added in 403.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2616 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 25 sheets defined 5.3% alpha, 40.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'D' and resid 5 through 10 removed outlier: 4.200A pdb=" N LEU D 9 " --> pdb=" O ASN D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 24 removed outlier: 4.177A pdb=" N ASN D 24 " --> pdb=" O SER D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 73 Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 116 through 120 Processing helix chain 'D' and resid 129 through 133 Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.752A pdb=" N ARG D 250 " --> pdb=" O ASP D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 448 removed outlier: 3.563A pdb=" N THR D 447 " --> pdb=" O ASN D 443 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR D 448 " --> pdb=" O PHE D 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 443 through 448' Processing helix chain 'D' and resid 817 through 822 removed outlier: 3.655A pdb=" N GLN D 821 " --> pdb=" O PRO D 818 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 36 Processing helix chain 'C' and resid 96 through 100 Processing helix chain 'C' and resid 125 through 129 removed outlier: 4.188A pdb=" N ALA C 128 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 69 Processing sheet with id=AA1, first strand: chain 'D' and resid 42 through 46 removed outlier: 5.002A pdb=" N TYR D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU D 39 " --> pdb=" O TYR D 43 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA D 45 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASP D 36 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU D 113 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TYR D 38 " --> pdb=" O LEU D 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'D' and resid 152 through 153 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 152 through 153 current: chain 'D' and resid 161 through 170 removed outlier: 4.308A pdb=" N ASN D 202 " --> pdb=" O ASN D 180 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR D 182 " --> pdb=" O HIS D 200 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N HIS D 200 " --> pdb=" O THR D 182 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N SER D 184 " --> pdb=" O TRP D 198 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TRP D 198 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 15.876A pdb=" N ILE D 201 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 10.076A pdb=" N TYR D 222 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N THR D 203 " --> pdb=" O ASP D 220 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N TYR D 331 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG D 376 " --> pdb=" O ASN D 400 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER D 407 " --> pdb=" O LEU D 403 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ILE D 429 " --> pdb=" O THR D 489 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR D 489 " --> pdb=" O ILE D 429 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU D 431 " --> pdb=" O THR D 487 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ARG D 481 " --> pdb=" O SER D 437 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY D 482 " --> pdb=" O THR D 506 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN D 647 " --> pdb=" O SER D 640 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 256 through 260 Processing sheet with id=AA5, first strand: chain 'D' and resid 273 through 280 removed outlier: 6.877A pdb=" N ILE D 268 " --> pdb=" O ILE D 275 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASN D 277 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL D 266 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR D 279 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA D 264 " --> pdb=" O THR D 279 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 700 through 701 Processing sheet with id=AA7, first strand: chain 'D' and resid 711 through 714 Processing sheet with id=AA8, first strand: chain 'D' and resid 725 through 726 Processing sheet with id=AA9, first strand: chain 'D' and resid 762 through 763 removed outlier: 6.935A pdb=" N LEU D 753 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N SER D 790 " --> pdb=" O LEU D 753 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N MET D 755 " --> pdb=" O TYR D 788 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TYR D 788 " --> pdb=" O MET D 755 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU D 757 " --> pdb=" O GLN D 786 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLN D 786 " --> pdb=" O LEU D 757 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 762 through 763 Processing sheet with id=AB2, first strand: chain 'D' and resid 778 through 780 Processing sheet with id=AB3, first strand: chain 'H' and resid 168 through 171 removed outlier: 3.541A pdb=" N VAL H 170 " --> pdb=" O THR F 6 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER F 3 " --> pdb=" O VAL H 274 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY F 9 " --> pdb=" O VAL H 268 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN H 191 " --> pdb=" O ALA H 242 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ALA H 242 " --> pdb=" O GLN H 191 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU H 193 " --> pdb=" O LEU H 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 18 through 20 removed outlier: 3.561A pdb=" N ALA F 19 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU F 52 " --> pdb=" O ALA F 19 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 23 through 24 removed outlier: 7.305A pdb=" N VAL C 9 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ARG C 116 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR C 11 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 114 through 116 removed outlier: 4.075A pdb=" N ALA F 145 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN C 104 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA F 147 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE F 149 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE C 108 " --> pdb=" O PHE F 149 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG C 110 " --> pdb=" O LEU F 151 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AB8, first strand: chain 'C' and resid 132 through 135 Processing sheet with id=AB9, first strand: chain 'C' and resid 160 through 161 removed outlier: 3.626A pdb=" N ARG C 160 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 152 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA C 165 " --> pdb=" O VAL C 152 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 160 through 161 removed outlier: 3.626A pdb=" N ARG C 160 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL C 152 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE C 190 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLU C 154 " --> pdb=" O ARG C 188 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARG C 188 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR C 187 " --> pdb=" O MET C 200 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AC3, first strand: chain 'H' and resid 16 through 22 removed outlier: 6.459A pdb=" N PHE H 142 " --> pdb=" O ARG H 132 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG H 132 " --> pdb=" O PHE H 142 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE H 144 " --> pdb=" O ILE H 130 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE H 130 " --> pdb=" O PHE H 144 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TRP H 146 " --> pdb=" O VAL H 128 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL H 128 " --> pdb=" O TRP H 146 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE H 148 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE H 126 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ALA H 63 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL H 128 " --> pdb=" O GLY H 61 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLY H 61 " --> pdb=" O VAL H 128 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE H 130 " --> pdb=" O GLN H 59 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 34 through 37 Processing sheet with id=AC5, first strand: chain 'H' and resid 117 through 120 removed outlier: 3.786A pdb=" N GLY H 117 " --> pdb=" O VAL H 156 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL H 154 " --> pdb=" O ALA H 119 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 178 through 181 removed outlier: 4.517A pdb=" N LEU H 252 " --> pdb=" O ILE H 181 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 184 through 185 422 hydrogen bonds defined for protein. 1083 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: 1.60 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3285 1.34 - 1.46: 2211 1.46 - 1.58: 3996 1.58 - 1.70: 0 1.70 - 1.82: 30 Bond restraints: 9522 Sorted by residual: bond pdb=" CB ASP C 78 " pdb=" CG ASP C 78 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.52e+00 bond pdb=" CB ASP D 134 " pdb=" CG ASP D 134 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.12e+00 bond pdb=" CB TRP D 183 " pdb=" CG TRP D 183 " ideal model delta sigma weight residual 1.498 1.527 -0.029 3.10e-02 1.04e+03 8.47e-01 bond pdb=" CB ASP C 192 " pdb=" CG ASP C 192 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.23e-01 bond pdb=" CA VAL D 16 " pdb=" CB VAL D 16 " ideal model delta sigma weight residual 1.548 1.538 0.010 1.13e-02 7.83e+03 7.24e-01 ... (remaining 9517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 12886 1.79 - 3.57: 161 3.57 - 5.36: 25 5.36 - 7.14: 3 7.14 - 8.93: 4 Bond angle restraints: 13079 Sorted by residual: angle pdb=" N ILE D 275 " pdb=" CA ILE D 275 " pdb=" C ILE D 275 " ideal model delta sigma weight residual 112.96 109.38 3.58 1.00e+00 1.00e+00 1.28e+01 angle pdb=" CB MET C 57 " pdb=" CG MET C 57 " pdb=" SD MET C 57 " ideal model delta sigma weight residual 112.70 120.67 -7.97 3.00e+00 1.11e-01 7.05e+00 angle pdb=" CA CYS D 810 " pdb=" CB CYS D 810 " pdb=" SG CYS D 810 " ideal model delta sigma weight residual 114.40 120.34 -5.94 2.30e+00 1.89e-01 6.67e+00 angle pdb=" CA LEU D 582 " pdb=" CB LEU D 582 " pdb=" CG LEU D 582 " ideal model delta sigma weight residual 116.30 125.23 -8.93 3.50e+00 8.16e-02 6.51e+00 angle pdb=" CA LEU H 172 " pdb=" CB LEU H 172 " pdb=" CG LEU H 172 " ideal model delta sigma weight residual 116.30 124.56 -8.26 3.50e+00 8.16e-02 5.56e+00 ... (remaining 13074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4950 17.91 - 35.82: 463 35.82 - 53.73: 97 53.73 - 71.64: 14 71.64 - 89.55: 4 Dihedral angle restraints: 5528 sinusoidal: 1431 harmonic: 4097 Sorted by residual: dihedral pdb=" CB CYS D 63 " pdb=" SG CYS D 63 " pdb=" SG CYS D 90 " pdb=" CB CYS D 90 " ideal model delta sinusoidal sigma weight residual 93.00 163.99 -70.99 1 1.00e+01 1.00e-02 6.47e+01 dihedral pdb=" CB CYS H 161 " pdb=" SG CYS H 161 " pdb=" SG CYS H 187 " pdb=" CB CYS H 187 " ideal model delta sinusoidal sigma weight residual 93.00 52.93 40.07 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" CA PHE D 525 " pdb=" C PHE D 525 " pdb=" N GLU D 526 " pdb=" CA GLU D 526 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 5525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 948 0.030 - 0.059: 395 0.059 - 0.089: 98 0.089 - 0.119: 112 0.119 - 0.148: 16 Chirality restraints: 1569 Sorted by residual: chirality pdb=" CA VAL D 320 " pdb=" N VAL D 320 " pdb=" C VAL D 320 " pdb=" CB VAL D 320 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CG LEU H 172 " pdb=" CB LEU H 172 " pdb=" CD1 LEU H 172 " pdb=" CD2 LEU H 172 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA ILE D 259 " pdb=" N ILE D 259 " pdb=" C ILE D 259 " pdb=" CB ILE D 259 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 1566 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 320 " 0.039 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO D 321 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 321 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 321 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 52 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO C 53 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 167 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" CG ASP H 167 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASP H 167 " 0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP H 167 " 0.009 2.00e-02 2.50e+03 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 918 2.75 - 3.29: 8369 3.29 - 3.83: 14033 3.83 - 4.36: 14405 4.36 - 4.90: 27039 Nonbonded interactions: 64764 Sorted by model distance: nonbonded pdb=" O THR C 189 " pdb=" OG1 THR C 197 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR H 226 " pdb=" OG1 THR H 253 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR D 375 " pdb=" O PHE D 442 " model vdw 2.245 3.040 nonbonded pdb=" O SER H 216 " pdb=" OG SER H 216 " model vdw 2.264 3.040 nonbonded pdb=" OD1 ASN C 39 " pdb=" N ALA C 40 " model vdw 2.309 3.120 ... (remaining 64759 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.240 Find NCS groups from input model: 0.040 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 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 : 0.002 0.036 9527 Z= 0.098 Angle : 0.537 8.927 13089 Z= 0.286 Chirality : 0.043 0.148 1569 Planarity : 0.003 0.060 1758 Dihedral : 14.608 89.553 2897 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.29 % Allowed : 32.65 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.22), residues: 1424 helix: -1.56 (0.77), residues: 49 sheet: 0.83 (0.21), residues: 625 loop : -0.40 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 8 TYR 0.014 0.001 TYR D 593 PHE 0.008 0.001 PHE D 525 TRP 0.009 0.001 TRP D 508 HIS 0.007 0.001 HIS D 809 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 9522) covalent geometry : angle 0.53628 (13079) SS BOND : bond 0.00427 ( 5) SS BOND : angle 1.08155 ( 10) hydrogen bonds : bond 0.14610 ( 419) hydrogen bonds : angle 6.25196 ( 1083) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 310 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 257 HIS cc_start: 0.6899 (m-70) cc_final: 0.6329 (m90) REVERT: D 324 GLN cc_start: 0.5958 (mm-40) cc_final: 0.5685 (mm110) REVERT: D 332 SER cc_start: 0.7158 (t) cc_final: 0.6880 (p) REVERT: D 379 ASN cc_start: 0.7299 (t0) cc_final: 0.7097 (m-40) REVERT: D 400 ASN cc_start: 0.8167 (m-40) cc_final: 0.7937 (t0) REVERT: D 416 PHE cc_start: 0.6806 (m-80) cc_final: 0.6591 (m-80) REVERT: D 484 LEU cc_start: 0.8478 (tp) cc_final: 0.8276 (tp) REVERT: D 518 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7818 (tm-30) REVERT: D 531 THR cc_start: 0.7266 (t) cc_final: 0.6973 (p) REVERT: D 537 THR cc_start: 0.7912 (m) cc_final: 0.7663 (p) REVERT: D 553 VAL cc_start: 0.8645 (t) cc_final: 0.8438 (m) REVERT: D 599 ASP cc_start: 0.7532 (t0) cc_final: 0.6966 (t0) REVERT: D 608 THR cc_start: 0.7986 (t) cc_final: 0.7493 (p) REVERT: D 636 ASN cc_start: 0.7805 (p0) cc_final: 0.7546 (p0) REVERT: D 669 LEU cc_start: 0.8051 (mp) cc_final: 0.7794 (mt) REVERT: D 688 ASN cc_start: 0.7389 (OUTLIER) cc_final: 0.7159 (m110) REVERT: D 756 THR cc_start: 0.8757 (m) cc_final: 0.8533 (p) REVERT: D 786 GLN cc_start: 0.7250 (mt0) cc_final: 0.6992 (mt0) REVERT: D 829 SER cc_start: 0.8534 (t) cc_final: 0.8168 (p) REVERT: F 4 THR cc_start: 0.8555 (m) cc_final: 0.8202 (p) REVERT: F 123 ASN cc_start: 0.7878 (t0) cc_final: 0.7514 (t0) REVERT: C 4 LEU cc_start: 0.8468 (mt) cc_final: 0.8191 (mp) REVERT: C 19 GLN cc_start: 0.7992 (mt0) cc_final: 0.7730 (mt0) REVERT: C 22 VAL cc_start: 0.8537 (t) cc_final: 0.8194 (p) REVERT: C 44 LYS cc_start: 0.9198 (tppp) cc_final: 0.8961 (mttm) REVERT: H 191 GLN cc_start: 0.8074 (pt0) cc_final: 0.7866 (pt0) outliers start: 2 outliers final: 0 residues processed: 310 average time/residue: 0.0910 time to fit residues: 39.4403 Evaluate side-chains 284 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 688 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 711 ASN D 809 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.131516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107175 restraints weight = 17359.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110407 restraints weight = 9673.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.112507 restraints weight = 6209.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.114036 restraints weight = 4452.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.114965 restraints weight = 3458.777| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9527 Z= 0.150 Angle : 0.581 9.732 13089 Z= 0.299 Chirality : 0.045 0.159 1569 Planarity : 0.004 0.060 1758 Dihedral : 3.433 16.403 1521 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 8.02 % Allowed : 29.01 % Favored : 62.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.23), residues: 1424 helix: -1.78 (0.78), residues: 44 sheet: 0.85 (0.20), residues: 640 loop : -0.29 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 258 TYR 0.017 0.002 TYR D 650 PHE 0.011 0.001 PHE D 4 TRP 0.013 0.002 TRP D 183 HIS 0.005 0.001 HIS D 504 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9522) covalent geometry : angle 0.58059 (13079) SS BOND : bond 0.00334 ( 5) SS BOND : angle 0.86890 ( 10) hydrogen bonds : bond 0.03389 ( 419) hydrogen bonds : angle 5.21839 ( 1083) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 290 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: D 237 GLN cc_start: 0.7977 (tt0) cc_final: 0.7775 (tt0) REVERT: D 240 SER cc_start: 0.8486 (m) cc_final: 0.8268 (m) REVERT: D 257 HIS cc_start: 0.7222 (m-70) cc_final: 0.6933 (m90) REVERT: D 324 GLN cc_start: 0.6729 (mm-40) cc_final: 0.6381 (mm-40) REVERT: D 332 SER cc_start: 0.7759 (t) cc_final: 0.7453 (p) REVERT: D 346 GLU cc_start: 0.7131 (mp0) cc_final: 0.6914 (mp0) REVERT: D 379 ASN cc_start: 0.7903 (t0) cc_final: 0.7500 (t0) REVERT: D 394 VAL cc_start: 0.8275 (p) cc_final: 0.7936 (m) REVERT: D 489 THR cc_start: 0.8257 (OUTLIER) cc_final: 0.7864 (p) REVERT: D 518 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7780 (tm-30) REVERT: D 531 THR cc_start: 0.7463 (t) cc_final: 0.7134 (p) REVERT: D 537 THR cc_start: 0.7982 (m) cc_final: 0.7647 (p) REVERT: D 599 ASP cc_start: 0.7880 (t70) cc_final: 0.7577 (t0) REVERT: D 608 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7499 (p) REVERT: D 636 ASN cc_start: 0.8008 (p0) cc_final: 0.7805 (p0) REVERT: D 647 GLN cc_start: 0.7445 (pt0) cc_final: 0.7073 (pt0) REVERT: D 669 LEU cc_start: 0.8496 (mp) cc_final: 0.8236 (mt) REVERT: D 683 ASP cc_start: 0.7699 (t0) cc_final: 0.7399 (t0) REVERT: D 688 ASN cc_start: 0.7885 (m110) cc_final: 0.7656 (m110) REVERT: D 706 THR cc_start: 0.8054 (p) cc_final: 0.7769 (t) REVERT: D 741 VAL cc_start: 0.8060 (t) cc_final: 0.7722 (p) REVERT: D 786 GLN cc_start: 0.7361 (mt0) cc_final: 0.7051 (mt0) REVERT: F 4 THR cc_start: 0.8583 (m) cc_final: 0.8204 (p) REVERT: F 123 ASN cc_start: 0.7935 (t0) cc_final: 0.7448 (t0) REVERT: C 4 LEU cc_start: 0.8543 (mt) cc_final: 0.8310 (mp) REVERT: C 75 LEU cc_start: 0.8204 (mm) cc_final: 0.7909 (mt) REVERT: C 151 THR cc_start: 0.8680 (m) cc_final: 0.8304 (p) REVERT: H 37 ASP cc_start: 0.6894 (OUTLIER) cc_final: 0.6581 (t0) REVERT: H 167 ASP cc_start: 0.7302 (t0) cc_final: 0.7015 (t0) REVERT: H 186 TYR cc_start: 0.7619 (p90) cc_final: 0.7362 (p90) REVERT: H 191 GLN cc_start: 0.8885 (pt0) cc_final: 0.8505 (pt0) REVERT: H 269 GLN cc_start: 0.8213 (tt0) cc_final: 0.7424 (tt0) REVERT: H 271 ILE cc_start: 0.8681 (mm) cc_final: 0.8364 (mm) outliers start: 55 outliers final: 27 residues processed: 315 average time/residue: 0.0773 time to fit residues: 35.1225 Evaluate side-chains 305 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 275 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 696 TRP Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 809 HIS Chi-restraints excluded: chain F residue 56 CYS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 239 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 8 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 124 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 588 ASN D 711 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.128115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102012 restraints weight = 17449.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105267 restraints weight = 9893.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107467 restraints weight = 6472.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.108950 restraints weight = 4696.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109884 restraints weight = 3722.935| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9527 Z= 0.183 Angle : 0.596 13.306 13089 Z= 0.309 Chirality : 0.046 0.187 1569 Planarity : 0.004 0.062 1758 Dihedral : 3.689 16.859 1519 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 7.87 % Allowed : 31.78 % Favored : 60.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.23), residues: 1424 helix: -1.76 (0.75), residues: 44 sheet: 0.78 (0.20), residues: 646 loop : -0.43 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 709 TYR 0.018 0.002 TYR D 338 PHE 0.027 0.002 PHE C 55 TRP 0.015 0.002 TRP D 204 HIS 0.010 0.002 HIS D 809 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9522) covalent geometry : angle 0.59563 (13079) SS BOND : bond 0.00292 ( 5) SS BOND : angle 0.75716 ( 10) hydrogen bonds : bond 0.03599 ( 419) hydrogen bonds : angle 5.23189 ( 1083) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 285 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: D 324 GLN cc_start: 0.6706 (mm-40) cc_final: 0.6421 (mm110) REVERT: D 328 HIS cc_start: 0.8072 (t-90) cc_final: 0.7853 (t-90) REVERT: D 379 ASN cc_start: 0.7944 (t0) cc_final: 0.7570 (t0) REVERT: D 386 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6826 (mtp) REVERT: D 416 PHE cc_start: 0.7306 (m-80) cc_final: 0.7093 (m-10) REVERT: D 484 LEU cc_start: 0.8534 (tp) cc_final: 0.8316 (tt) REVERT: D 489 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.7945 (p) REVERT: D 518 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7835 (tm-30) REVERT: D 537 THR cc_start: 0.7929 (m) cc_final: 0.7587 (p) REVERT: D 557 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7763 (m-10) REVERT: D 588 ASN cc_start: 0.8405 (m-40) cc_final: 0.8169 (m-40) REVERT: D 599 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7702 (t0) REVERT: D 608 THR cc_start: 0.7920 (t) cc_final: 0.7420 (p) REVERT: D 647 GLN cc_start: 0.7488 (pt0) cc_final: 0.7110 (pt0) REVERT: D 669 LEU cc_start: 0.8517 (mp) cc_final: 0.8298 (mt) REVERT: D 683 ASP cc_start: 0.7735 (t0) cc_final: 0.7378 (t0) REVERT: D 688 ASN cc_start: 0.7925 (m110) cc_final: 0.7666 (m110) REVERT: D 706 THR cc_start: 0.8140 (p) cc_final: 0.7939 (t) REVERT: D 728 ASN cc_start: 0.7663 (t0) cc_final: 0.7422 (t0) REVERT: D 741 VAL cc_start: 0.8132 (t) cc_final: 0.7891 (p) REVERT: D 786 GLN cc_start: 0.7349 (mt0) cc_final: 0.7099 (mt0) REVERT: F 4 THR cc_start: 0.8628 (m) cc_final: 0.8265 (p) REVERT: F 64 LYS cc_start: 0.8343 (ttmm) cc_final: 0.8098 (mttm) REVERT: F 65 VAL cc_start: 0.9098 (OUTLIER) cc_final: 0.8711 (p) REVERT: F 123 ASN cc_start: 0.7963 (t0) cc_final: 0.7416 (t0) REVERT: C 55 PHE cc_start: 0.8205 (p90) cc_final: 0.7955 (p90) REVERT: C 75 LEU cc_start: 0.8268 (mm) cc_final: 0.7962 (mt) REVERT: C 151 THR cc_start: 0.8663 (m) cc_final: 0.8263 (p) REVERT: H 37 ASP cc_start: 0.6964 (OUTLIER) cc_final: 0.6640 (t0) REVERT: H 167 ASP cc_start: 0.7343 (t0) cc_final: 0.7012 (t0) REVERT: H 186 TYR cc_start: 0.7617 (p90) cc_final: 0.7360 (p90) REVERT: H 191 GLN cc_start: 0.8921 (pt0) cc_final: 0.8508 (pt0) REVERT: H 269 GLN cc_start: 0.8360 (tt0) cc_final: 0.7962 (tt0) outliers start: 54 outliers final: 33 residues processed: 305 average time/residue: 0.0860 time to fit residues: 37.4542 Evaluate side-chains 318 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 279 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 599 ASP Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 696 TRP Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 718 ASN Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain F residue 56 CYS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 149 TYR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 231 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.852 > 50: distance: 95 - 157: 13.838 distance: 98 - 154: 16.032 distance: 113 - 144: 35.964 distance: 116 - 141: 12.849 distance: 131 - 134: 6.496 distance: 134 - 135: 6.071 distance: 135 - 136: 5.807 distance: 135 - 138: 5.357 distance: 136 - 137: 5.974 distance: 136 - 141: 14.872 distance: 138 - 139: 23.735 distance: 138 - 140: 9.283 distance: 142 - 143: 19.018 distance: 142 - 145: 27.321 distance: 143 - 144: 34.042 distance: 143 - 146: 22.277 distance: 146 - 147: 19.964 distance: 147 - 148: 13.026 distance: 147 - 150: 15.152 distance: 148 - 149: 24.458 distance: 148 - 154: 19.333 distance: 151 - 152: 7.454 distance: 154 - 155: 6.029 distance: 155 - 156: 5.417 distance: 155 - 158: 4.752 distance: 156 - 157: 7.832 distance: 156 - 161: 9.410 distance: 158 - 159: 20.380 distance: 158 - 160: 29.061 distance: 161 - 162: 8.517 distance: 162 - 163: 9.858 distance: 162 - 165: 8.567 distance: 163 - 164: 13.860 distance: 163 - 168: 5.322 distance: 165 - 166: 26.034 distance: 165 - 167: 17.800 distance: 168 - 169: 14.983 distance: 168 - 174: 14.345 distance: 169 - 172: 16.193 distance: 170 - 171: 27.164 distance: 170 - 175: 8.343 distance: 172 - 173: 11.589 distance: 173 - 174: 8.091 distance: 175 - 176: 12.242 distance: 176 - 177: 5.782 distance: 176 - 179: 14.785 distance: 177 - 178: 16.775 distance: 177 - 182: 3.091 distance: 179 - 180: 21.073 distance: 179 - 181: 43.191 distance: 182 - 183: 16.171 distance: 183 - 184: 14.335 distance: 183 - 186: 17.126 distance: 184 - 185: 12.756 distance: 184 - 193: 15.155 distance: 186 - 187: 25.414 distance: 187 - 188: 22.342 distance: 188 - 189: 19.055 distance: 189 - 190: 18.831 distance: 190 - 191: 4.840 distance: 190 - 192: 11.631 distance: 193 - 194: 11.455 distance: 194 - 195: 10.769 distance: 195 - 196: 20.296 distance: 195 - 197: 5.346 distance: 197 - 198: 3.028 distance: 198 - 199: 16.553 distance: 198 - 201: 11.331 distance: 199 - 200: 11.805 distance: 199 - 202: 5.819