Starting phenix.real_space_refine on Sat Aug 23 23:56:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dn3_27553/08_2025/8dn3_27553_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dn3_27553/08_2025/8dn3_27553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dn3_27553/08_2025/8dn3_27553_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dn3_27553/08_2025/8dn3_27553_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dn3_27553/08_2025/8dn3_27553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dn3_27553/08_2025/8dn3_27553.map" } resolution = 3.55 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= 0.008 sd= 0.086 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: 5 Type Number sf(0) Gaussians S 102 5.16 5 Cl 2 4.86 5 C 9467 2.51 5 N 2270 2.21 5 O 2474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 14315 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 2762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2762 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain breaks: 1 Chain: "A" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2796 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 15, 'TRANS': 327} Chain breaks: 1 Chain: "B" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2768 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 15, 'TRANS': 324} Chain breaks: 1 Chain: "C" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2785 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2707 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 107 Unusual residues: {'DD9': 1, 'HEX': 3, 'HP6': 2, 'NAG': 1, 'NBU': 2, 'UND': 4} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 103 Unusual residues: {'DD9': 2, 'HEX': 4, 'HP6': 2, 'NAG': 1, 'UND': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 81 Unusual residues: {'DD9': 5, 'HEX': 3, 'NAG': 1, 'NBU': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 116 Unusual residues: {'D10': 1, 'DD9': 3, 'HEX': 3, 'HP6': 2, 'NAG': 1, 'UND': 3} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 90 Unusual residues: {' CL': 2, 'DD9': 2, 'HEX': 2, 'HP6': 2, 'NAG': 1, 'NBU': 2, 'UND': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.50, per 1000 atoms: 0.24 Number of scatterers: 14315 At special positions: 0 Unit cell: (103.75, 127.82, 132.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 102 16.00 O 2474 8.00 N 2270 7.00 C 9467 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 175 " distance=2.03 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=5, symmetry=0 Links applied NAG-ASN " NAG C 503 " - " ASN C 38 " " NAG D 501 " - " ASN D 38 " " NAG E 504 " - " ASN E 220 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 693.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3252 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 13 sheets defined 38.9% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'D' and resid 9 through 18 removed outlier: 3.536A pdb=" N LEU D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 220 through 243 Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 248 through 274 removed outlier: 4.049A pdb=" N ALA D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 311 removed outlier: 3.962A pdb=" N TRP D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N HIS D 311 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 419 removed outlier: 4.280A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY D 401 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE D 402 " --> pdb=" O SER D 398 " (cutoff:3.500A) Proline residue: D 403 - end of helix Processing helix chain 'A' and resid 9 through 18 Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 86 through 93 removed outlier: 3.617A pdb=" N LEU A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 93 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 228 through 243 Processing helix chain 'A' and resid 248 through 271 removed outlier: 3.620A pdb=" N ARG A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 311 removed outlier: 3.798A pdb=" N HIS A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 419 removed outlier: 3.961A pdb=" N ILE A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 9 through 18 Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 221 through 243 Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 248 through 274 removed outlier: 3.602A pdb=" N ARG B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 310 Processing helix chain 'B' and resid 385 through 419 removed outlier: 3.789A pdb=" N ILE B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Proline residue: B 403 - end of helix removed outlier: 3.625A pdb=" N TRP B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 415 " --> pdb=" O MET B 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 18 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 220 through 241 Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 248 through 274 Processing helix chain 'C' and resid 283 through 313 removed outlier: 3.919A pdb=" N HIS C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS C 312 " --> pdb=" O SER C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 417 removed outlier: 3.748A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Proline residue: C 403 - end of helix Processing helix chain 'E' and resid 34 through 43 removed outlier: 3.614A pdb=" N LEU E 38 " --> pdb=" O THR E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 95 Processing helix chain 'E' and resid 112 through 116 removed outlier: 3.520A pdb=" N LEU E 116 " --> pdb=" O TYR E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 170 Processing helix chain 'E' and resid 244 through 251 Processing helix chain 'E' and resid 251 through 265 removed outlier: 3.820A pdb=" N SER E 265 " --> pdb=" O LEU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 268 No H-bonds generated for 'chain 'E' and resid 266 through 268' Processing helix chain 'E' and resid 272 through 295 Proline residue: E 278 - end of helix Processing helix chain 'E' and resid 305 through 333 Processing helix chain 'E' and resid 448 through 475 removed outlier: 3.805A pdb=" N ALA E 457 " --> pdb=" O LEU E 453 " (cutoff:3.500A) Proline residue: E 460 - end of helix Processing sheet with id=AA1, first strand: chain 'D' and resid 37 through 45 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 37 through 45 current: chain 'D' and resid 57 through 68 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 57 through 68 current: chain 'D' and resid 126 through 134 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 98 through 100 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 149 through 158 current: chain 'D' and resid 205 through 217 Processing sheet with id=AA3, first strand: chain 'A' and resid 37 through 44 removed outlier: 6.533A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 65 through 69 current: chain 'A' and resid 116 through 121 removed outlier: 4.523A pdb=" N ASN A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 49 through 52 removed outlier: 5.181A pdb=" N SER A 50 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG A 59 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 57 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS A 107 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 98 through 100 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 151 through 158 current: chain 'A' and resid 205 through 217 Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 44 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 37 through 44 current: chain 'B' and resid 57 through 69 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 57 through 69 current: chain 'B' and resid 125 through 137 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 99 through 100 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 149 through 157 current: chain 'B' and resid 205 through 217 Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 52 removed outlier: 7.071A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE C 44 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 69 current: chain 'C' and resid 125 through 134 Processing sheet with id=AA9, first strand: chain 'C' and resid 98 through 100 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 149 through 158 current: chain 'C' and resid 206 through 217 Processing sheet with id=AB1, first strand: chain 'E' and resid 105 through 106 removed outlier: 4.464A pdb=" N ASP E 148 " --> pdb=" O PHE E 144 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASP E 78 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N SER E 71 " --> pdb=" O ASP E 78 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ARG E 80 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N PHE E 69 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN E 82 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN E 90 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP E 59 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL E 58 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ILE E 192 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL E 60 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 121 through 123 Processing sheet with id=AB3, first strand: chain 'E' and resid 172 through 176 Processing sheet with id=AB4, first strand: chain 'E' and resid 223 through 225 removed outlier: 3.540A pdb=" N LYS E 223 " --> pdb=" O TYR E 231 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR E 225 " --> pdb=" O GLY E 229 " (cutoff:3.500A) 529 hydrogen bonds defined for protein. 1551 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: 1.75 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4181 1.34 - 1.46: 2289 1.46 - 1.57: 7965 1.57 - 1.69: 0 1.69 - 1.81: 172 Bond restraints: 14607 Sorted by residual: bond pdb=" N GLN D 310 " pdb=" CA GLN D 310 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.87e+00 bond pdb=" N VAL C 37 " pdb=" CA VAL C 37 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.18e+00 bond pdb=" N VAL D 37 " pdb=" CA VAL D 37 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.23e-02 6.61e+03 7.41e+00 bond pdb=" N ILE A 257 " pdb=" CA ILE A 257 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.35e+00 bond pdb=" N LYS A 312 " pdb=" CA LYS A 312 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.45e+00 ... (remaining 14602 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 19189 1.66 - 3.32: 352 3.32 - 4.97: 58 4.97 - 6.63: 10 6.63 - 8.29: 3 Bond angle restraints: 19612 Sorted by residual: angle pdb=" N ARG B 309 " pdb=" CA ARG B 309 " pdb=" C ARG B 309 " ideal model delta sigma weight residual 112.89 107.11 5.78 1.24e+00 6.50e-01 2.17e+01 angle pdb=" CA HIS A 311 " pdb=" C HIS A 311 " pdb=" O HIS A 311 " ideal model delta sigma weight residual 121.19 117.38 3.81 1.10e+00 8.26e-01 1.20e+01 angle pdb=" CA THR A 258 " pdb=" C THR A 258 " pdb=" O THR A 258 " ideal model delta sigma weight residual 120.82 117.49 3.33 1.05e+00 9.07e-01 1.01e+01 angle pdb=" N GLN A 310 " pdb=" CA GLN A 310 " pdb=" C GLN A 310 " ideal model delta sigma weight residual 111.71 108.07 3.64 1.15e+00 7.56e-01 1.00e+01 angle pdb=" N PHE D 412 " pdb=" CA PHE D 412 " pdb=" C PHE D 412 " ideal model delta sigma weight residual 112.89 109.00 3.89 1.24e+00 6.50e-01 9.85e+00 ... (remaining 19607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 8530 24.23 - 48.47: 273 48.47 - 72.70: 18 72.70 - 96.93: 11 96.93 - 121.16: 6 Dihedral angle restraints: 8838 sinusoidal: 3821 harmonic: 5017 Sorted by residual: dihedral pdb=" C3 DD9 A 508 " pdb=" C4 DD9 A 508 " pdb=" C5 DD9 A 508 " pdb=" C6 DD9 A 508 " ideal model delta sinusoidal sigma weight residual 179.92 58.76 121.16 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" C1 DD9 A 508 " pdb=" C2 DD9 A 508 " pdb=" C3 DD9 A 508 " pdb=" C4 DD9 A 508 " ideal model delta sinusoidal sigma weight residual 179.94 -67.82 -112.24 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C2 NAG E 504 " pdb=" C3 NAG E 504 " pdb=" C4 NAG E 504 " pdb=" C5 NAG E 504 " ideal model delta sinusoidal sigma weight residual 53.78 -48.09 101.87 1 3.00e+01 1.11e-03 1.29e+01 ... (remaining 8835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.173: 2154 0.173 - 0.346: 1 0.346 - 0.519: 0 0.519 - 0.692: 0 0.692 - 0.865: 1 Chirality restraints: 2156 Sorted by residual: chirality pdb=" C1 NAG D 501 " pdb=" ND2 ASN D 38 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.54 -0.86 2.00e-01 2.50e+01 1.87e+01 chirality pdb=" C1 NAG E 504 " pdb=" ND2 ASN E 220 " pdb=" C2 NAG E 504 " pdb=" O5 NAG E 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA VAL C 37 " pdb=" N VAL C 37 " pdb=" C VAL C 37 " pdb=" CB VAL C 37 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.97e-01 ... (remaining 2153 not shown) Planarity restraints: 2415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 501 " 0.321 2.00e-02 2.50e+03 2.74e-01 9.37e+02 pdb=" C7 NAG A 501 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG A 501 " -0.003 2.00e-02 2.50e+03 pdb=" N2 NAG A 501 " -0.466 2.00e-02 2.50e+03 pdb=" O7 NAG A 501 " 0.221 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 501 " -0.292 2.00e-02 2.50e+03 2.48e-01 7.68e+02 pdb=" C7 NAG D 501 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG D 501 " -0.178 2.00e-02 2.50e+03 pdb=" N2 NAG D 501 " 0.429 2.00e-02 2.50e+03 pdb=" O7 NAG D 501 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 503 " -0.281 2.00e-02 2.50e+03 2.35e-01 6.90e+02 pdb=" C7 NAG C 503 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG C 503 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG C 503 " 0.396 2.00e-02 2.50e+03 pdb=" O7 NAG C 503 " -0.008 2.00e-02 2.50e+03 ... (remaining 2412 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 661 2.73 - 3.27: 14154 3.27 - 3.81: 22580 3.81 - 4.36: 26996 4.36 - 4.90: 46970 Nonbonded interactions: 111361 Sorted by model distance: nonbonded pdb=" O LEU A 98 " pdb=" OG1 THR B 112 " model vdw 2.181 3.040 nonbonded pdb=" O ALA D 282 " pdb=" OH TYR D 413 " model vdw 2.222 3.040 nonbonded pdb=" OG1 THR A 112 " pdb=" O LEU E 121 " model vdw 2.234 3.040 nonbonded pdb=" O LEU B 98 " pdb=" OG1 THR C 112 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR B 162 " pdb=" OD1 ASN B 164 " model vdw 2.238 3.040 ... (remaining 111356 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 310 or resid 384 through 386 or (resid 387 and ( \ name N or name CA or name C or name O or name CB )) or resid 388 through 419)) selection = (chain 'B' and (resid 9 through 310 or resid 384 through 386 or (resid 387 and ( \ name N or name CA or name C or name O or name CB )) or resid 388 through 419)) selection = (chain 'C' and (resid 9 through 310 or resid 384 through 419)) selection = (chain 'D' and (resid 9 through 310 or resid 384 through 386 or (resid 387 and ( \ name N or name CA or name C or name O or name CB )) or resid 388 through 419)) } 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 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: 2.390 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.530 Find NCS groups from input model: 0.200 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.006 0.423 14624 Z= 0.494 Angle : 0.570 8.288 19639 Z= 0.288 Chirality : 0.046 0.865 2156 Planarity : 0.009 0.274 2412 Dihedral : 11.886 121.162 5559 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.87 % Favored : 96.01 % Rotamer: Outliers : 1.97 % Allowed : 5.51 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.22), residues: 1679 helix: 2.25 (0.22), residues: 583 sheet: -0.40 (0.30), residues: 359 loop : -0.75 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 271 TYR 0.017 0.001 TYR E 325 PHE 0.010 0.001 PHE D 242 TRP 0.008 0.001 TRP D 243 HIS 0.002 0.000 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00343 (14607) covalent geometry : angle 0.56471 (19612) SS BOND : bond 0.00105 ( 9) SS BOND : angle 0.63481 ( 18) hydrogen bonds : bond 0.13217 ( 529) hydrogen bonds : angle 5.77662 ( 1551) Misc. bond : bond 0.24770 ( 5) link_NAG-ASN : bond 0.00574 ( 3) link_NAG-ASN : angle 3.72745 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 332 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8081 (t70) cc_final: 0.7671 (p0) REVERT: D 246 MET cc_start: 0.7313 (mtm) cc_final: 0.7076 (mtt) REVERT: A 91 ASP cc_start: 0.8812 (t0) cc_final: 0.8612 (t0) REVERT: A 169 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7849 (mt-10) REVERT: A 173 GLN cc_start: 0.8343 (pp30) cc_final: 0.8086 (pp30) REVERT: A 203 ASN cc_start: 0.8690 (m-40) cc_final: 0.8006 (p0) REVERT: A 396 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7571 (mtmm) REVERT: A 400 ILE cc_start: 0.8271 (tp) cc_final: 0.7582 (pt) REVERT: B 18 MET cc_start: 0.8467 (ppp) cc_final: 0.8112 (ptt) REVERT: B 83 LEU cc_start: 0.7978 (tt) cc_final: 0.7710 (tt) REVERT: B 397 ILE cc_start: 0.8516 (mm) cc_final: 0.8249 (mt) REVERT: B 411 MET cc_start: 0.7501 (mmp) cc_final: 0.6547 (ttp) REVERT: C 191 GLU cc_start: 0.8209 (tp30) cc_final: 0.7933 (tp30) REVERT: E 176 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8196 (mmtt) REVERT: E 187 ASP cc_start: 0.8308 (t0) cc_final: 0.7799 (t0) REVERT: E 329 GLN cc_start: 0.8469 (tp40) cc_final: 0.8204 (tp40) outliers start: 30 outliers final: 12 residues processed: 357 average time/residue: 0.1074 time to fit residues: 57.1160 Evaluate side-chains 261 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 249 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain E residue 167 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 ASN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN D 201 HIS A 125 ASN E 243 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.131874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.104772 restraints weight = 21381.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.108670 restraints weight = 10601.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.111323 restraints weight = 6768.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.113093 restraints weight = 5057.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.114061 restraints weight = 4176.299| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14624 Z= 0.179 Angle : 0.612 9.964 19639 Z= 0.303 Chirality : 0.045 0.371 2156 Planarity : 0.004 0.039 2412 Dihedral : 6.955 68.248 2242 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.41 % Favored : 95.53 % Rotamer: Outliers : 2.56 % Allowed : 11.02 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.21), residues: 1679 helix: 2.08 (0.21), residues: 593 sheet: -0.60 (0.29), residues: 379 loop : -0.79 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 399 TYR 0.021 0.002 TYR A 301 PHE 0.011 0.001 PHE B 48 TRP 0.014 0.001 TRP B 243 HIS 0.003 0.001 HIS D 311 Details of bonding type rmsd covalent geometry : bond 0.00426 (14607) covalent geometry : angle 0.60836 (19612) SS BOND : bond 0.00125 ( 9) SS BOND : angle 0.80775 ( 18) hydrogen bonds : bond 0.04845 ( 529) hydrogen bonds : angle 5.19239 ( 1551) Misc. bond : bond 0.00099 ( 5) link_NAG-ASN : bond 0.00203 ( 3) link_NAG-ASN : angle 3.20326 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 262 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8096 (t70) cc_final: 0.7728 (p0) REVERT: D 246 MET cc_start: 0.7415 (mtm) cc_final: 0.7171 (mtt) REVERT: D 263 MET cc_start: 0.8577 (mmm) cc_final: 0.8131 (tmm) REVERT: D 298 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7808 (tt) REVERT: A 169 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7750 (mt-10) REVERT: A 173 GLN cc_start: 0.8422 (pp30) cc_final: 0.8122 (pp30) REVERT: A 203 ASN cc_start: 0.8637 (m-40) cc_final: 0.8026 (p0) REVERT: A 220 MET cc_start: 0.7518 (mmm) cc_final: 0.7189 (mmm) REVERT: A 396 LYS cc_start: 0.8190 (mmtt) cc_final: 0.7563 (mtmm) REVERT: A 400 ILE cc_start: 0.8502 (tp) cc_final: 0.7841 (pt) REVERT: A 411 MET cc_start: 0.6845 (mmp) cc_final: 0.6429 (mmp) REVERT: B 18 MET cc_start: 0.8465 (ppp) cc_final: 0.8228 (ptt) REVERT: B 83 LEU cc_start: 0.8119 (tt) cc_final: 0.7799 (tt) REVERT: B 397 ILE cc_start: 0.8539 (mm) cc_final: 0.8275 (mt) REVERT: B 411 MET cc_start: 0.7622 (mmp) cc_final: 0.6558 (ttp) REVERT: C 206 LYS cc_start: 0.7367 (mptt) cc_final: 0.6803 (ttpt) REVERT: E 176 LYS cc_start: 0.8670 (mmtt) cc_final: 0.8208 (mmtt) REVERT: E 187 ASP cc_start: 0.8338 (t0) cc_final: 0.7797 (t0) REVERT: E 331 MET cc_start: 0.8140 (mmp) cc_final: 0.7898 (mmm) outliers start: 39 outliers final: 30 residues processed: 286 average time/residue: 0.0926 time to fit residues: 40.6090 Evaluate side-chains 269 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 132 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 119 optimal weight: 0.3980 chunk 139 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 HIS D 201 HIS C 46 ASN E 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.130178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.102815 restraints weight = 21628.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.106695 restraints weight = 10783.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.109333 restraints weight = 6912.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.111105 restraints weight = 5173.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.112194 restraints weight = 4274.178| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14624 Z= 0.184 Angle : 0.596 10.334 19639 Z= 0.299 Chirality : 0.044 0.307 2156 Planarity : 0.004 0.038 2412 Dihedral : 6.237 54.269 2229 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.29 % Favored : 95.65 % Rotamer: Outliers : 3.67 % Allowed : 11.74 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.21), residues: 1679 helix: 2.12 (0.21), residues: 593 sheet: -0.64 (0.29), residues: 377 loop : -0.88 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 271 TYR 0.023 0.002 TYR A 301 PHE 0.012 0.001 PHE B 48 TRP 0.019 0.001 TRP C 243 HIS 0.003 0.001 HIS D 311 Details of bonding type rmsd covalent geometry : bond 0.00444 (14607) covalent geometry : angle 0.59326 (19612) SS BOND : bond 0.00134 ( 9) SS BOND : angle 0.82950 ( 18) hydrogen bonds : bond 0.04825 ( 529) hydrogen bonds : angle 5.11582 ( 1551) Misc. bond : bond 0.00022 ( 5) link_NAG-ASN : bond 0.00517 ( 3) link_NAG-ASN : angle 2.79871 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 244 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8125 (t70) cc_final: 0.7746 (p0) REVERT: D 246 MET cc_start: 0.7452 (mtm) cc_final: 0.7185 (mtt) REVERT: D 263 MET cc_start: 0.8559 (mmm) cc_final: 0.8340 (mmm) REVERT: D 298 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7825 (tt) REVERT: A 169 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7734 (mt-10) REVERT: A 173 GLN cc_start: 0.8443 (pp30) cc_final: 0.8118 (pp30) REVERT: A 203 ASN cc_start: 0.8652 (m-40) cc_final: 0.8031 (p0) REVERT: A 220 MET cc_start: 0.7547 (mmm) cc_final: 0.7337 (mmm) REVERT: A 243 TRP cc_start: 0.7271 (m100) cc_final: 0.7063 (m100) REVERT: A 396 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7547 (mtmm) REVERT: A 400 ILE cc_start: 0.8517 (tp) cc_final: 0.7889 (pt) REVERT: A 411 MET cc_start: 0.6804 (mmp) cc_final: 0.6412 (mmp) REVERT: B 18 MET cc_start: 0.8510 (ppp) cc_final: 0.8263 (ptt) REVERT: B 83 LEU cc_start: 0.8149 (tt) cc_final: 0.7744 (tt) REVERT: B 397 ILE cc_start: 0.8463 (mm) cc_final: 0.8124 (mt) REVERT: B 411 MET cc_start: 0.7678 (mmp) cc_final: 0.7414 (mmp) REVERT: C 206 LYS cc_start: 0.7373 (mptt) cc_final: 0.6747 (mtmt) REVERT: E 176 LYS cc_start: 0.8666 (mmtt) cc_final: 0.8134 (mmtt) REVERT: E 187 ASP cc_start: 0.8395 (t0) cc_final: 0.7848 (t0) REVERT: E 248 MET cc_start: 0.8814 (tpp) cc_final: 0.8349 (tpp) REVERT: E 329 GLN cc_start: 0.8751 (tp40) cc_final: 0.8393 (tp40) outliers start: 56 outliers final: 39 residues processed: 279 average time/residue: 0.1006 time to fit residues: 42.7181 Evaluate side-chains 267 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 227 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 1 optimal weight: 0.0770 chunk 96 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 159 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 201 HIS ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.133126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.106218 restraints weight = 21414.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.110216 restraints weight = 10489.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.112949 restraints weight = 6643.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.114758 restraints weight = 4929.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.115942 restraints weight = 4051.971| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14624 Z= 0.104 Angle : 0.551 9.344 19639 Z= 0.272 Chirality : 0.043 0.249 2156 Planarity : 0.003 0.038 2412 Dihedral : 5.743 56.956 2229 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.99 % Favored : 95.95 % Rotamer: Outliers : 3.21 % Allowed : 13.51 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.21), residues: 1679 helix: 2.27 (0.21), residues: 594 sheet: -0.52 (0.29), residues: 383 loop : -0.80 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 271 TYR 0.018 0.001 TYR D 301 PHE 0.012 0.001 PHE E 84 TRP 0.022 0.001 TRP C 243 HIS 0.002 0.000 HIS D 311 Details of bonding type rmsd covalent geometry : bond 0.00227 (14607) covalent geometry : angle 0.54885 (19612) SS BOND : bond 0.00153 ( 9) SS BOND : angle 0.68730 ( 18) hydrogen bonds : bond 0.04050 ( 529) hydrogen bonds : angle 4.83425 ( 1551) Misc. bond : bond 0.00018 ( 5) link_NAG-ASN : bond 0.00527 ( 3) link_NAG-ASN : angle 2.50991 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 256 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8114 (t70) cc_final: 0.7614 (p0) REVERT: D 246 MET cc_start: 0.7435 (mtm) cc_final: 0.7176 (mtt) REVERT: D 263 MET cc_start: 0.8450 (mmm) cc_final: 0.7997 (tmm) REVERT: D 298 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7940 (tt) REVERT: A 173 GLN cc_start: 0.8451 (pp30) cc_final: 0.8125 (pp30) REVERT: A 203 ASN cc_start: 0.8631 (m-40) cc_final: 0.8038 (p0) REVERT: A 220 MET cc_start: 0.7449 (mmm) cc_final: 0.7193 (mmm) REVERT: A 243 TRP cc_start: 0.7049 (m100) cc_final: 0.6724 (m100) REVERT: A 396 LYS cc_start: 0.8028 (mmtt) cc_final: 0.7457 (mtmm) REVERT: A 400 ILE cc_start: 0.8442 (tp) cc_final: 0.7809 (pt) REVERT: A 411 MET cc_start: 0.6883 (mmt) cc_final: 0.6523 (mmp) REVERT: B 18 MET cc_start: 0.8451 (ppp) cc_final: 0.8228 (ptt) REVERT: B 83 LEU cc_start: 0.8092 (tt) cc_final: 0.7698 (tt) REVERT: B 266 GLN cc_start: 0.8171 (tp40) cc_final: 0.7911 (tt0) REVERT: B 411 MET cc_start: 0.7570 (mmp) cc_final: 0.6522 (ttp) REVERT: C 56 MET cc_start: 0.8267 (mmt) cc_final: 0.8067 (mmt) REVERT: E 77 MET cc_start: 0.8656 (mmt) cc_final: 0.8323 (mmt) REVERT: E 176 LYS cc_start: 0.8664 (mmtt) cc_final: 0.8160 (mmtt) REVERT: E 187 ASP cc_start: 0.8360 (t0) cc_final: 0.7834 (t0) REVERT: E 248 MET cc_start: 0.8702 (tpp) cc_final: 0.8336 (tpp) outliers start: 49 outliers final: 34 residues processed: 291 average time/residue: 0.0974 time to fit residues: 43.3442 Evaluate side-chains 272 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 60 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 201 HIS C 42 ASN E 243 GLN E 333 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.133432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.106425 restraints weight = 21399.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.110414 restraints weight = 10529.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.113148 restraints weight = 6680.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.114956 restraints weight = 4962.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.116041 restraints weight = 4078.569| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14624 Z= 0.109 Angle : 0.545 9.545 19639 Z= 0.267 Chirality : 0.042 0.224 2156 Planarity : 0.003 0.040 2412 Dihedral : 5.606 59.490 2229 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.67 % Allowed : 14.43 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.21), residues: 1679 helix: 2.34 (0.21), residues: 594 sheet: -0.63 (0.28), residues: 395 loop : -0.76 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 271 TYR 0.027 0.001 TYR E 224 PHE 0.018 0.001 PHE C 13 TRP 0.024 0.001 TRP C 243 HIS 0.007 0.001 HIS D 311 Details of bonding type rmsd covalent geometry : bond 0.00248 (14607) covalent geometry : angle 0.54306 (19612) SS BOND : bond 0.00141 ( 9) SS BOND : angle 0.64522 ( 18) hydrogen bonds : bond 0.03933 ( 529) hydrogen bonds : angle 4.77157 ( 1551) Misc. bond : bond 0.00015 ( 5) link_NAG-ASN : bond 0.00531 ( 3) link_NAG-ASN : angle 2.29313 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 243 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8124 (t70) cc_final: 0.7610 (p0) REVERT: D 246 MET cc_start: 0.7405 (mtm) cc_final: 0.7145 (mtt) REVERT: A 173 GLN cc_start: 0.8469 (pp30) cc_final: 0.8129 (pp30) REVERT: A 203 ASN cc_start: 0.8644 (m-40) cc_final: 0.8044 (p0) REVERT: A 220 MET cc_start: 0.7612 (mmm) cc_final: 0.7280 (mmm) REVERT: A 243 TRP cc_start: 0.7088 (m100) cc_final: 0.6811 (m100) REVERT: A 396 LYS cc_start: 0.8007 (mmtt) cc_final: 0.7450 (mtmm) REVERT: A 400 ILE cc_start: 0.8400 (tp) cc_final: 0.7749 (pt) REVERT: A 411 MET cc_start: 0.6874 (mmt) cc_final: 0.6483 (mmp) REVERT: B 83 LEU cc_start: 0.8101 (tt) cc_final: 0.7716 (tt) REVERT: B 411 MET cc_start: 0.7532 (mmp) cc_final: 0.6469 (ttp) REVERT: E 77 MET cc_start: 0.8662 (mmt) cc_final: 0.8383 (mmt) REVERT: E 141 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7989 (tt) REVERT: E 176 LYS cc_start: 0.8654 (mmtt) cc_final: 0.8022 (mmtt) REVERT: E 187 ASP cc_start: 0.8372 (t0) cc_final: 0.7851 (t0) REVERT: E 248 MET cc_start: 0.8635 (tpp) cc_final: 0.8312 (tpp) outliers start: 56 outliers final: 42 residues processed: 282 average time/residue: 0.0961 time to fit residues: 41.2670 Evaluate side-chains 274 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 231 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 91 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 166 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN E 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.133896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.106987 restraints weight = 21347.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.110955 restraints weight = 10459.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.113700 restraints weight = 6631.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.115506 restraints weight = 4916.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.116711 restraints weight = 4038.576| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14624 Z= 0.106 Angle : 0.546 9.571 19639 Z= 0.266 Chirality : 0.042 0.209 2156 Planarity : 0.004 0.079 2412 Dihedral : 5.515 59.973 2229 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.67 % Allowed : 15.02 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.58 (0.21), residues: 1679 helix: 2.36 (0.21), residues: 594 sheet: -0.59 (0.29), residues: 395 loop : -0.74 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 271 TYR 0.024 0.001 TYR E 224 PHE 0.012 0.001 PHE C 13 TRP 0.020 0.001 TRP D 243 HIS 0.005 0.001 HIS D 311 Details of bonding type rmsd covalent geometry : bond 0.00240 (14607) covalent geometry : angle 0.54363 (19612) SS BOND : bond 0.00156 ( 9) SS BOND : angle 0.63684 ( 18) hydrogen bonds : bond 0.03842 ( 529) hydrogen bonds : angle 4.72769 ( 1551) Misc. bond : bond 0.00017 ( 5) link_NAG-ASN : bond 0.00512 ( 3) link_NAG-ASN : angle 2.19432 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 239 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8119 (t70) cc_final: 0.7585 (p0) REVERT: D 246 MET cc_start: 0.7387 (mtm) cc_final: 0.7126 (mtt) REVERT: A 56 MET cc_start: 0.8241 (mmt) cc_final: 0.7849 (mmt) REVERT: A 169 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7663 (mt-10) REVERT: A 173 GLN cc_start: 0.8484 (pp30) cc_final: 0.8133 (pp30) REVERT: A 203 ASN cc_start: 0.8634 (m-40) cc_final: 0.8029 (p0) REVERT: A 220 MET cc_start: 0.7461 (mmm) cc_final: 0.7246 (mmm) REVERT: A 243 TRP cc_start: 0.7017 (m100) cc_final: 0.6753 (m100) REVERT: A 396 LYS cc_start: 0.7971 (mmtt) cc_final: 0.7431 (mtmm) REVERT: A 400 ILE cc_start: 0.8424 (tp) cc_final: 0.7757 (pt) REVERT: A 411 MET cc_start: 0.6853 (mmt) cc_final: 0.6488 (mmp) REVERT: B 83 LEU cc_start: 0.8115 (tt) cc_final: 0.7729 (tt) REVERT: B 411 MET cc_start: 0.7459 (mmp) cc_final: 0.6404 (ttp) REVERT: C 42 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8369 (p0) REVERT: E 77 MET cc_start: 0.8672 (mmt) cc_final: 0.8434 (mmt) REVERT: E 141 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8032 (tt) REVERT: E 176 LYS cc_start: 0.8658 (mmtt) cc_final: 0.8042 (mmtt) REVERT: E 187 ASP cc_start: 0.8376 (t0) cc_final: 0.7858 (t0) REVERT: E 248 MET cc_start: 0.8627 (tpp) cc_final: 0.8360 (tpp) REVERT: E 329 GLN cc_start: 0.8567 (tp40) cc_final: 0.8320 (tp40) outliers start: 56 outliers final: 43 residues processed: 278 average time/residue: 0.0942 time to fit residues: 40.2346 Evaluate side-chains 279 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 234 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 114 optimal weight: 0.0570 chunk 159 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 156 optimal weight: 0.4980 chunk 157 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.135251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.108068 restraints weight = 21171.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.112122 restraints weight = 10426.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.114895 restraints weight = 6610.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.116737 restraints weight = 4898.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.117829 restraints weight = 4018.467| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14624 Z= 0.100 Angle : 0.545 9.441 19639 Z= 0.264 Chirality : 0.042 0.195 2156 Planarity : 0.004 0.058 2412 Dihedral : 5.415 58.894 2229 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.54 % Allowed : 15.93 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.21), residues: 1679 helix: 2.34 (0.21), residues: 596 sheet: -0.59 (0.28), residues: 395 loop : -0.70 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 271 TYR 0.017 0.001 TYR D 301 PHE 0.022 0.001 PHE C 13 TRP 0.020 0.001 TRP D 243 HIS 0.004 0.000 HIS D 311 Details of bonding type rmsd covalent geometry : bond 0.00223 (14607) covalent geometry : angle 0.54303 (19612) SS BOND : bond 0.00162 ( 9) SS BOND : angle 0.61366 ( 18) hydrogen bonds : bond 0.03737 ( 529) hydrogen bonds : angle 4.67634 ( 1551) Misc. bond : bond 0.00017 ( 5) link_NAG-ASN : bond 0.00504 ( 3) link_NAG-ASN : angle 2.07704 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 251 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8123 (t70) cc_final: 0.7573 (p0) REVERT: D 246 MET cc_start: 0.7350 (mtm) cc_final: 0.7091 (mtt) REVERT: A 56 MET cc_start: 0.8216 (mmt) cc_final: 0.7823 (mmt) REVERT: A 75 TYR cc_start: 0.8319 (p90) cc_final: 0.7944 (p90) REVERT: A 169 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7662 (mt-10) REVERT: A 173 GLN cc_start: 0.8485 (pp30) cc_final: 0.8133 (pp30) REVERT: A 203 ASN cc_start: 0.8644 (m-40) cc_final: 0.8018 (p0) REVERT: A 220 MET cc_start: 0.7604 (mmm) cc_final: 0.7270 (mmm) REVERT: A 243 TRP cc_start: 0.6964 (m100) cc_final: 0.6710 (m100) REVERT: A 396 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7455 (mtmm) REVERT: A 400 ILE cc_start: 0.8462 (tp) cc_final: 0.7788 (pt) REVERT: A 411 MET cc_start: 0.6854 (mmt) cc_final: 0.6473 (mmp) REVERT: B 83 LEU cc_start: 0.8121 (tt) cc_final: 0.7741 (tt) REVERT: B 411 MET cc_start: 0.7404 (mmp) cc_final: 0.6380 (ttp) REVERT: C 42 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8052 (p0) REVERT: E 77 MET cc_start: 0.8663 (mmt) cc_final: 0.8374 (mmt) REVERT: E 141 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8054 (tt) REVERT: E 187 ASP cc_start: 0.8378 (t0) cc_final: 0.7857 (t0) REVERT: E 249 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7464 (ttm) REVERT: E 329 GLN cc_start: 0.8583 (tp40) cc_final: 0.8307 (tp40) outliers start: 54 outliers final: 43 residues processed: 287 average time/residue: 0.0902 time to fit residues: 39.6382 Evaluate side-chains 285 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 239 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 70 optimal weight: 1.9990 chunk 99 optimal weight: 0.0870 chunk 121 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 64 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN C 46 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.134353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.107057 restraints weight = 21282.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.111088 restraints weight = 10487.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.113829 restraints weight = 6665.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.115638 restraints weight = 4958.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.116735 restraints weight = 4079.654| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14624 Z= 0.112 Angle : 0.553 9.638 19639 Z= 0.269 Chirality : 0.042 0.188 2156 Planarity : 0.004 0.066 2412 Dihedral : 5.422 58.862 2229 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.15 % Allowed : 16.72 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.21), residues: 1679 helix: 2.30 (0.21), residues: 596 sheet: -0.64 (0.28), residues: 402 loop : -0.66 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 271 TYR 0.018 0.001 TYR A 301 PHE 0.013 0.001 PHE C 13 TRP 0.022 0.001 TRP D 243 HIS 0.003 0.000 HIS D 311 Details of bonding type rmsd covalent geometry : bond 0.00258 (14607) covalent geometry : angle 0.55142 (19612) SS BOND : bond 0.00166 ( 9) SS BOND : angle 0.64526 ( 18) hydrogen bonds : bond 0.03807 ( 529) hydrogen bonds : angle 4.68970 ( 1551) Misc. bond : bond 0.00019 ( 5) link_NAG-ASN : bond 0.00503 ( 3) link_NAG-ASN : angle 2.02610 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 240 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8118 (t70) cc_final: 0.7579 (p0) REVERT: D 246 MET cc_start: 0.7347 (mtm) cc_final: 0.7069 (mtt) REVERT: A 56 MET cc_start: 0.8223 (mmt) cc_final: 0.7876 (mmt) REVERT: A 169 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7665 (mt-10) REVERT: A 173 GLN cc_start: 0.8503 (pp30) cc_final: 0.8140 (pp30) REVERT: A 203 ASN cc_start: 0.8616 (m-40) cc_final: 0.8007 (p0) REVERT: A 220 MET cc_start: 0.7613 (mmm) cc_final: 0.7251 (mmm) REVERT: A 243 TRP cc_start: 0.7019 (m100) cc_final: 0.6765 (m100) REVERT: A 396 LYS cc_start: 0.8021 (mmtt) cc_final: 0.7473 (mtmm) REVERT: A 400 ILE cc_start: 0.8452 (tp) cc_final: 0.7765 (pt) REVERT: A 411 MET cc_start: 0.6842 (mmt) cc_final: 0.6462 (mmp) REVERT: B 83 LEU cc_start: 0.8143 (tt) cc_final: 0.7748 (tt) REVERT: B 411 MET cc_start: 0.7373 (mmp) cc_final: 0.6346 (ttp) REVERT: C 42 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8194 (p0) REVERT: E 77 MET cc_start: 0.8658 (mmt) cc_final: 0.8421 (mmt) REVERT: E 187 ASP cc_start: 0.8391 (t0) cc_final: 0.7870 (t0) REVERT: E 248 MET cc_start: 0.8524 (tpp) cc_final: 0.8222 (mmm) REVERT: E 329 GLN cc_start: 0.8594 (tp40) cc_final: 0.8287 (tp40) outliers start: 48 outliers final: 43 residues processed: 269 average time/residue: 0.0910 time to fit residues: 37.7845 Evaluate side-chains 275 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 231 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 27 optimal weight: 0.0060 chunk 106 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 186 GLN D 201 HIS C 42 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.130655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.102891 restraints weight = 21512.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.106759 restraints weight = 10868.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.109404 restraints weight = 7030.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.111154 restraints weight = 5294.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.112229 restraints weight = 4392.854| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14624 Z= 0.198 Angle : 0.609 10.530 19639 Z= 0.302 Chirality : 0.044 0.172 2156 Planarity : 0.004 0.048 2412 Dihedral : 6.037 59.184 2229 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.28 % Allowed : 17.44 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.21), residues: 1679 helix: 2.22 (0.21), residues: 594 sheet: -0.72 (0.28), residues: 398 loop : -0.74 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 271 TYR 0.025 0.002 TYR A 301 PHE 0.014 0.001 PHE A 295 TRP 0.030 0.001 TRP D 243 HIS 0.003 0.001 HIS D 311 Details of bonding type rmsd covalent geometry : bond 0.00480 (14607) covalent geometry : angle 0.60787 (19612) SS BOND : bond 0.00181 ( 9) SS BOND : angle 0.83527 ( 18) hydrogen bonds : bond 0.04633 ( 529) hydrogen bonds : angle 4.90822 ( 1551) Misc. bond : bond 0.00015 ( 5) link_NAG-ASN : bond 0.00495 ( 3) link_NAG-ASN : angle 1.92955 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 228 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 141 ASP cc_start: 0.8116 (t70) cc_final: 0.7616 (p0) REVERT: D 246 MET cc_start: 0.7395 (mtm) cc_final: 0.7122 (mtt) REVERT: D 263 MET cc_start: 0.8573 (mmm) cc_final: 0.8174 (mmm) REVERT: A 169 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7717 (mt-10) REVERT: A 173 GLN cc_start: 0.8523 (pp30) cc_final: 0.8150 (pp30) REVERT: A 203 ASN cc_start: 0.8647 (m-40) cc_final: 0.8046 (p0) REVERT: A 220 MET cc_start: 0.7736 (mmm) cc_final: 0.7413 (mmm) REVERT: A 227 MET cc_start: 0.8509 (mmt) cc_final: 0.8116 (mmt) REVERT: A 396 LYS cc_start: 0.8063 (mmtt) cc_final: 0.7520 (mtmm) REVERT: A 400 ILE cc_start: 0.8534 (tp) cc_final: 0.7865 (pt) REVERT: A 411 MET cc_start: 0.6936 (mmt) cc_final: 0.6568 (mmp) REVERT: B 83 LEU cc_start: 0.8197 (tt) cc_final: 0.7750 (tt) REVERT: C 42 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8191 (p0) REVERT: E 77 MET cc_start: 0.8702 (mmt) cc_final: 0.8464 (mmt) REVERT: E 141 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8199 (tt) REVERT: E 187 ASP cc_start: 0.8450 (t0) cc_final: 0.7912 (t0) REVERT: E 316 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8337 (mp) outliers start: 50 outliers final: 42 residues processed: 262 average time/residue: 0.0917 time to fit residues: 37.1057 Evaluate side-chains 267 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 243 TRP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 67.3433 > 50: distance: 20 - 24: 19.037 distance: 24 - 25: 28.113 distance: 24 - 30: 23.078 distance: 25 - 26: 42.810 distance: 26 - 27: 24.776 distance: 26 - 31: 19.233 distance: 28 - 29: 13.908 distance: 29 - 30: 34.159 distance: 31 - 32: 33.721 distance: 32 - 33: 45.850 distance: 32 - 35: 29.624 distance: 33 - 34: 47.318 distance: 33 - 39: 41.358 distance: 35 - 36: 55.405 distance: 36 - 37: 33.229 distance: 36 - 38: 28.317 distance: 40 - 41: 37.423 distance: 40 - 43: 41.425 distance: 41 - 42: 49.685 distance: 41 - 47: 4.681 distance: 43 - 44: 7.507 distance: 44 - 45: 43.730 distance: 44 - 46: 20.141 distance: 47 - 48: 30.830 distance: 48 - 49: 23.799 distance: 48 - 51: 28.027 distance: 49 - 50: 39.087 distance: 49 - 55: 12.928 distance: 51 - 52: 6.214 distance: 52 - 53: 39.675 distance: 52 - 54: 41.567 distance: 55 - 56: 36.970 distance: 56 - 57: 36.457 distance: 56 - 59: 30.412 distance: 57 - 58: 53.724 distance: 57 - 62: 14.424 distance: 59 - 60: 57.572 distance: 59 - 61: 47.912 distance: 62 - 63: 22.617 distance: 63 - 64: 46.268 distance: 63 - 66: 14.520 distance: 64 - 65: 40.591 distance: 64 - 70: 22.776 distance: 65 - 88: 25.389 distance: 66 - 67: 34.016 distance: 67 - 68: 4.881 distance: 70 - 71: 41.651 distance: 71 - 72: 47.227 distance: 71 - 74: 29.014 distance: 72 - 73: 60.999 distance: 72 - 81: 44.805 distance: 74 - 75: 15.382 distance: 75 - 76: 20.641 distance: 75 - 77: 17.667 distance: 76 - 78: 15.478 distance: 77 - 79: 12.614 distance: 78 - 80: 13.975 distance: 79 - 80: 13.393 distance: 81 - 82: 36.552 distance: 81 - 87: 30.554 distance: 82 - 83: 18.747 distance: 82 - 85: 28.695 distance: 83 - 84: 31.449 distance: 83 - 88: 17.019 distance: 85 - 86: 12.691 distance: 86 - 87: 21.866 distance: 88 - 89: 27.235 distance: 89 - 90: 19.952 distance: 89 - 92: 28.031 distance: 90 - 91: 41.821 distance: 90 - 96: 20.836 distance: 92 - 93: 30.962 distance: 93 - 94: 21.134 distance: 94 - 95: 17.055 distance: 96 - 97: 26.309 distance: 97 - 98: 24.114 distance: 97 - 100: 17.167 distance: 98 - 99: 23.996 distance: 98 - 104: 20.642 distance: 100 - 101: 12.348 distance: 101 - 102: 32.204 distance: 101 - 103: 16.122