Starting phenix.real_space_refine on Fri Aug 22 20:16:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ind_60703/08_2025/9ind_60703.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ind_60703/08_2025/9ind_60703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ind_60703/08_2025/9ind_60703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ind_60703/08_2025/9ind_60703.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ind_60703/08_2025/9ind_60703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ind_60703/08_2025/9ind_60703.map" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4854 2.51 5 N 1269 2.21 5 O 1484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s 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: 7644 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3267 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 21, 'TRANS': 418} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 9, 'ARG:plan': 4, 'GLU:plan': 6, 'GLN:plan1': 2, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "H" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 913 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 116} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 782 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 96} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2565 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 139 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 12, 'GLN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 3, 'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 117 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.64, per 1000 atoms: 0.21 Number of scatterers: 7644 At special positions: 0 Unit cell: (72.15, 95.55, 126.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1484 8.00 N 1269 7.00 C 4854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 128 " distance=2.02 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 377 " 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=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A 501 " - " ASN A 44 " " NAG A 502 " - " ASN A 260 " " NAG B 501 " - " ASN B 389 " " NAG B 502 " - " ASN B 414 " " NAG C 1 " - " ASN A 266 " Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 406.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1838 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 19 sheets defined 14.4% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.511A pdb=" N THR A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.794A pdb=" N LYS A 370 " --> pdb=" O GLU A 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.912A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.987A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 123 Processing helix chain 'B' and resid 126 through 135 removed outlier: 4.593A pdb=" N SER B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 172 removed outlier: 3.598A pdb=" N ILE B 165 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR B 172 " --> pdb=" O GLN B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 202 removed outlier: 3.580A pdb=" N PHE B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 224 removed outlier: 3.638A pdb=" N GLN B 220 " --> pdb=" O ASP B 216 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 250 through 256 removed outlier: 3.920A pdb=" N LYS B 253 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 293 removed outlier: 3.642A pdb=" N LYS B 289 " --> pdb=" O GLN B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 313 removed outlier: 3.747A pdb=" N TYR B 309 " --> pdb=" O GLN B 305 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 313 " --> pdb=" O TYR B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 345 removed outlier: 3.511A pdb=" N VAL B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 343 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 345 " --> pdb=" O LYS B 341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.527A pdb=" N TYR A 11 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A 431 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ASP A 421 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 411 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 407 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81 removed outlier: 7.200A pdb=" N ASP A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 98 through 101 removed outlier: 3.556A pdb=" N LYS A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.519A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 225 through 229 removed outlier: 3.701A pdb=" N SER A 225 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE A 255 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 280 through 283 Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 348 removed outlier: 5.650A pdb=" N ASP A 357 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN A 389 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AB3, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 11 removed outlier: 4.110A pdb=" N GLY H 33 " --> pdb=" O ASN H 99 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.611A pdb=" N TYR H 108 " --> pdb=" O LEU H 98 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N TYR H 100 " --> pdb=" O PHE H 106 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N PHE H 106 " --> pdb=" O TYR H 100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 6 through 7 removed outlier: 3.629A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.615A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LYS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU L 33 " --> pdb=" O LYS L 49 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AB9, first strand: chain 'B' and resid 80 through 82 removed outlier: 6.428A pdb=" N VAL B 81 " --> pdb=" O HIS B 420 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 182 through 189 removed outlier: 7.040A pdb=" N VAL B 185 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N SER B 148 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N SER B 187 " --> pdb=" O PHE B 146 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N PHE B 146 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TYR B 103 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP B 141 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU B 237 " --> pdb=" O PRO B 104 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP B 106 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU B 239 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR B 108 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N MET B 241 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU B 110 " --> pdb=" O MET B 241 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N ILE B 320 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 297 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLY B 322 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N PHE B 299 " --> pdb=" O GLY B 322 " (cutoff:3.500A) 260 hydrogen bonds defined for protein. 669 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: 0.74 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1865 1.33 - 1.45: 1808 1.45 - 1.57: 4090 1.57 - 1.70: 0 1.70 - 1.82: 57 Bond restraints: 7820 Sorted by residual: bond pdb=" C GLN B 168 " pdb=" N CYS B 169 " ideal model delta sigma weight residual 1.335 1.242 0.093 1.31e-02 5.83e+03 5.03e+01 bond pdb=" N ASN B 173 " pdb=" CA ASN B 173 " ideal model delta sigma weight residual 1.462 1.395 0.066 1.44e-02 4.82e+03 2.12e+01 bond pdb=" CA ASN B 173 " pdb=" C ASN B 173 " ideal model delta sigma weight residual 1.528 1.500 0.028 1.04e-02 9.25e+03 7.31e+00 bond pdb=" C5 MAN C 4 " pdb=" O5 MAN C 4 " ideal model delta sigma weight residual 1.418 1.470 -0.052 2.00e-02 2.50e+03 6.75e+00 bond pdb=" CA ASN B 173 " pdb=" CB ASN B 173 " ideal model delta sigma weight residual 1.526 1.488 0.038 1.51e-02 4.39e+03 6.39e+00 ... (remaining 7815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 10182 2.35 - 4.69: 403 4.69 - 7.04: 46 7.04 - 9.38: 15 9.38 - 11.73: 6 Bond angle restraints: 10652 Sorted by residual: angle pdb=" O GLN B 168 " pdb=" C GLN B 168 " pdb=" N CYS B 169 " ideal model delta sigma weight residual 122.15 111.65 10.50 1.14e+00 7.69e-01 8.48e+01 angle pdb=" O ASN B 167 " pdb=" C ASN B 167 " pdb=" N GLN B 168 " ideal model delta sigma weight residual 122.27 133.39 -11.12 1.23e+00 6.61e-01 8.18e+01 angle pdb=" CA ASN B 167 " pdb=" C ASN B 167 " pdb=" N GLN B 168 " ideal model delta sigma weight residual 117.72 105.99 11.73 1.31e+00 5.83e-01 8.01e+01 angle pdb=" C GLN B 168 " pdb=" N CYS B 169 " pdb=" CA CYS B 169 " ideal model delta sigma weight residual 120.28 131.75 -11.47 1.34e+00 5.57e-01 7.32e+01 angle pdb=" CA GLN B 168 " pdb=" C GLN B 168 " pdb=" N CYS B 169 " ideal model delta sigma weight residual 117.39 127.88 -10.49 1.24e+00 6.50e-01 7.16e+01 ... (remaining 10647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 4562 21.89 - 43.78: 114 43.78 - 65.68: 8 65.68 - 87.57: 10 87.57 - 109.46: 7 Dihedral angle restraints: 4701 sinusoidal: 1815 harmonic: 2886 Sorted by residual: dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual -86.00 -4.27 -81.73 1 1.00e+01 1.00e-02 8.22e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 160.44 -67.44 1 1.00e+01 1.00e-02 5.92e+01 dihedral pdb=" CA ASN H 99 " pdb=" C ASN H 99 " pdb=" N TYR H 100 " pdb=" CA TYR H 100 " ideal model delta harmonic sigma weight residual 180.00 148.76 31.24 0 5.00e+00 4.00e-02 3.90e+01 ... (remaining 4698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 845 0.058 - 0.115: 287 0.115 - 0.172: 69 0.172 - 0.229: 11 0.229 - 0.287: 4 Chirality restraints: 1216 Sorted by residual: chirality pdb=" CB ILE A 433 " pdb=" CA ILE A 433 " pdb=" CG1 ILE A 433 " pdb=" CG2 ILE A 433 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.37 0.03 2.00e-02 2.50e+03 1.77e+00 chirality pdb=" CB VAL B 348 " pdb=" CA VAL B 348 " pdb=" CG1 VAL B 348 " pdb=" CG2 VAL B 348 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1213 not shown) Planarity restraints: 1385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 294 " -0.025 2.00e-02 2.50e+03 2.55e-02 1.14e+01 pdb=" CG PHE A 294 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 294 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A 294 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 294 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE A 294 " -0.020 2.00e-02 2.50e+03 pdb=" CZ PHE A 294 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 114 " 0.019 2.00e-02 2.50e+03 1.68e-02 7.04e+00 pdb=" CG TRP A 114 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 114 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 114 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 114 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 114 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 114 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 114 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 114 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 114 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 272 " 0.017 2.00e-02 2.50e+03 1.74e-02 6.05e+00 pdb=" CG TYR B 272 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR B 272 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 272 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 272 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 272 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 272 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 272 " 0.002 2.00e-02 2.50e+03 ... (remaining 1382 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1963 2.79 - 3.32: 6258 3.32 - 3.85: 13035 3.85 - 4.37: 15722 4.37 - 4.90: 26957 Nonbonded interactions: 63935 Sorted by model distance: nonbonded pdb=" OD1 ASN A 377 " pdb=" OG SER A 388 " model vdw 2.266 3.040 nonbonded pdb=" OG SER A 279 " pdb=" O SER A 342 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR A 275 " pdb=" OD1 ASP B 251 " model vdw 2.297 3.040 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.308 3.040 nonbonded pdb=" NE2 GLN A 156 " pdb=" O LEU B 254 " model vdw 2.335 3.120 ... (remaining 63930 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.870 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:7.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 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 : 0.011 0.099 7837 Z= 0.479 Angle : 1.106 11.728 10695 Z= 0.626 Chirality : 0.062 0.287 1216 Planarity : 0.007 0.055 1380 Dihedral : 11.527 109.461 2839 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.26 % Allowed : 1.30 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.25 (0.22), residues: 1000 helix: -4.46 (0.24), residues: 96 sheet: -1.53 (0.24), residues: 372 loop : -2.15 (0.22), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG A 115 TYR 0.043 0.004 TYR B 272 PHE 0.054 0.004 PHE A 294 TRP 0.046 0.005 TRP A 114 HIS 0.011 0.003 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.01078 ( 7820) covalent geometry : angle 1.09034 (10652) SS BOND : bond 0.00553 ( 8) SS BOND : angle 2.04865 ( 16) hydrogen bonds : bond 0.24352 ( 254) hydrogen bonds : angle 11.13241 ( 669) link_ALPHA1-3 : bond 0.00114 ( 1) link_ALPHA1-3 : angle 2.66754 ( 3) link_ALPHA1-6 : bond 0.01601 ( 1) link_ALPHA1-6 : angle 2.40823 ( 3) link_BETA1-4 : bond 0.00938 ( 2) link_BETA1-4 : angle 4.69997 ( 6) link_NAG-ASN : bond 0.00735 ( 5) link_NAG-ASN : angle 3.53512 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 0.167 Fit side-chains REVERT: A 46 THR cc_start: 0.7771 (t) cc_final: 0.7545 (m) REVERT: A 232 ASN cc_start: 0.8049 (p0) cc_final: 0.7776 (p0) REVERT: A 406 TYR cc_start: 0.8080 (t80) cc_final: 0.7732 (t80) REVERT: A 408 MET cc_start: 0.7470 (mtm) cc_final: 0.7253 (ptp) REVERT: A 427 PHE cc_start: 0.7750 (p90) cc_final: 0.7500 (p90) REVERT: A 438 ARG cc_start: 0.6759 (mtm180) cc_final: 0.5819 (tmt170) REVERT: L 36 TYR cc_start: 0.8201 (m-80) cc_final: 0.7964 (m-80) REVERT: L 48 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7452 (mm) REVERT: B 179 PRO cc_start: 0.7759 (Cg_endo) cc_final: 0.7429 (Cg_exo) REVERT: B 223 VAL cc_start: 0.8401 (p) cc_final: 0.8191 (t) REVERT: B 244 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7617 (mm110) REVERT: B 251 ASP cc_start: 0.7897 (m-30) cc_final: 0.7672 (m-30) REVERT: B 259 VAL cc_start: 0.8101 (p) cc_final: 0.7765 (t) REVERT: B 311 ASP cc_start: 0.7873 (m-30) cc_final: 0.7631 (m-30) outliers start: 2 outliers final: 0 residues processed: 218 average time/residue: 0.3082 time to fit residues: 72.3969 Evaluate side-chains 195 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 131 GLN A 207 GLN A 271 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 42 GLN ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN B 270 ASN B 340 GLN B 360 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.119790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.108392 restraints weight = 10317.316| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.60 r_work: 0.3318 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 7837 Z= 0.220 Angle : 0.686 8.146 10695 Z= 0.359 Chirality : 0.049 0.207 1216 Planarity : 0.005 0.037 1380 Dihedral : 9.936 89.538 1264 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.38 % Allowed : 10.00 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.24), residues: 1000 helix: -2.75 (0.37), residues: 96 sheet: -0.82 (0.26), residues: 364 loop : -1.71 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 38 TYR 0.022 0.002 TYR H 32 PHE 0.031 0.003 PHE A 294 TRP 0.016 0.003 TRP A 114 HIS 0.006 0.002 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 7820) covalent geometry : angle 0.67236 (10652) SS BOND : bond 0.00363 ( 8) SS BOND : angle 1.71861 ( 16) hydrogen bonds : bond 0.04275 ( 254) hydrogen bonds : angle 7.29718 ( 669) link_ALPHA1-3 : bond 0.01158 ( 1) link_ALPHA1-3 : angle 3.08091 ( 3) link_ALPHA1-6 : bond 0.01278 ( 1) link_ALPHA1-6 : angle 1.59148 ( 3) link_BETA1-4 : bond 0.00382 ( 2) link_BETA1-4 : angle 2.68877 ( 6) link_NAG-ASN : bond 0.00521 ( 5) link_NAG-ASN : angle 2.42202 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.164 Fit side-chains REVERT: A 46 THR cc_start: 0.7991 (t) cc_final: 0.7754 (m) REVERT: A 168 ARG cc_start: 0.7747 (mtp85) cc_final: 0.7367 (mtt-85) REVERT: A 232 ASN cc_start: 0.7978 (p0) cc_final: 0.7491 (p0) REVERT: A 376 PHE cc_start: 0.7943 (m-80) cc_final: 0.7640 (m-80) REVERT: A 438 ARG cc_start: 0.7172 (mtm180) cc_final: 0.5991 (tmt170) REVERT: H 46 GLU cc_start: 0.7756 (tp30) cc_final: 0.7167 (tp30) REVERT: L 36 TYR cc_start: 0.8291 (m-80) cc_final: 0.8052 (m-80) REVERT: L 52 SER cc_start: 0.8451 (OUTLIER) cc_final: 0.8187 (m) REVERT: L 86 TYR cc_start: 0.8272 (m-80) cc_final: 0.8019 (m-80) REVERT: B 203 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7205 (mtmp) REVERT: B 251 ASP cc_start: 0.8229 (m-30) cc_final: 0.7976 (m-30) REVERT: B 258 VAL cc_start: 0.8409 (m) cc_final: 0.8101 (t) REVERT: B 259 VAL cc_start: 0.8263 (p) cc_final: 0.7996 (t) REVERT: B 278 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7167 (mtt) REVERT: B 348 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8172 (t) outliers start: 26 outliers final: 8 residues processed: 204 average time/residue: 0.3273 time to fit residues: 72.1500 Evaluate side-chains 203 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 285 GLN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 5 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 77 ASN A 314 GLN A 356 ASN H 111 GLN L 42 GLN B 92 ASN B 166 HIS B 244 GLN B 340 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.109933 restraints weight = 10082.612| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.55 r_work: 0.3333 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7837 Z= 0.219 Angle : 0.672 9.696 10695 Z= 0.344 Chirality : 0.049 0.229 1216 Planarity : 0.005 0.035 1380 Dihedral : 8.714 72.477 1262 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.94 % Allowed : 11.56 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.25), residues: 1000 helix: -1.31 (0.46), residues: 96 sheet: -0.32 (0.26), residues: 368 loop : -1.42 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 78 TYR 0.027 0.002 TYR H 32 PHE 0.020 0.002 PHE A 294 TRP 0.021 0.003 TRP A 395 HIS 0.007 0.002 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 7820) covalent geometry : angle 0.65917 (10652) SS BOND : bond 0.00303 ( 8) SS BOND : angle 1.54119 ( 16) hydrogen bonds : bond 0.04039 ( 254) hydrogen bonds : angle 6.68512 ( 669) link_ALPHA1-3 : bond 0.01630 ( 1) link_ALPHA1-3 : angle 2.65973 ( 3) link_ALPHA1-6 : bond 0.01437 ( 1) link_ALPHA1-6 : angle 1.38281 ( 3) link_BETA1-4 : bond 0.00365 ( 2) link_BETA1-4 : angle 2.70846 ( 6) link_NAG-ASN : bond 0.00420 ( 5) link_NAG-ASN : angle 2.50999 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.186 Fit side-chains REVERT: A 46 THR cc_start: 0.7945 (t) cc_final: 0.7711 (m) REVERT: A 168 ARG cc_start: 0.7684 (mtp85) cc_final: 0.7396 (mtt-85) REVERT: A 232 ASN cc_start: 0.7815 (p0) cc_final: 0.7302 (p0) REVERT: A 438 ARG cc_start: 0.7207 (mtm180) cc_final: 0.5999 (tmt170) REVERT: H 46 GLU cc_start: 0.7932 (tp30) cc_final: 0.7352 (tp30) REVERT: L 86 TYR cc_start: 0.8305 (m-80) cc_final: 0.7899 (m-80) REVERT: L 102 THR cc_start: 0.8656 (t) cc_final: 0.8392 (t) REVERT: B 72 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7523 (mt) REVERT: B 203 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7374 (mtmp) REVERT: B 226 SER cc_start: 0.8093 (OUTLIER) cc_final: 0.7868 (m) REVERT: B 251 ASP cc_start: 0.8210 (m-30) cc_final: 0.7978 (m-30) REVERT: B 258 VAL cc_start: 0.8334 (m) cc_final: 0.8077 (t) REVERT: B 259 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.7944 (t) REVERT: B 278 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.7151 (mtt) REVERT: B 348 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8182 (t) REVERT: B 390 VAL cc_start: 0.8006 (t) cc_final: 0.7695 (m) outliers start: 38 outliers final: 14 residues processed: 202 average time/residue: 0.3145 time to fit residues: 68.4502 Evaluate side-chains 201 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 285 GLN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 90 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 314 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN B 200 HIS B 244 GLN B 340 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.121933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.110687 restraints weight = 10326.645| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.55 r_work: 0.3336 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7837 Z= 0.175 Angle : 0.627 9.834 10695 Z= 0.319 Chirality : 0.047 0.210 1216 Planarity : 0.004 0.042 1380 Dihedral : 7.492 57.431 1262 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.16 % Allowed : 14.68 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.26), residues: 1000 helix: -0.66 (0.51), residues: 96 sheet: -0.11 (0.27), residues: 363 loop : -1.24 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 78 TYR 0.020 0.002 TYR L 50 PHE 0.015 0.002 PHE B 142 TRP 0.017 0.002 TRP A 395 HIS 0.005 0.002 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 7820) covalent geometry : angle 0.61587 (10652) SS BOND : bond 0.00380 ( 8) SS BOND : angle 1.29756 ( 16) hydrogen bonds : bond 0.03533 ( 254) hydrogen bonds : angle 6.42931 ( 669) link_ALPHA1-3 : bond 0.01934 ( 1) link_ALPHA1-3 : angle 2.30351 ( 3) link_ALPHA1-6 : bond 0.01659 ( 1) link_ALPHA1-6 : angle 1.12219 ( 3) link_BETA1-4 : bond 0.00335 ( 2) link_BETA1-4 : angle 2.52045 ( 6) link_NAG-ASN : bond 0.00312 ( 5) link_NAG-ASN : angle 2.27216 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 46 THR cc_start: 0.7939 (t) cc_final: 0.7710 (m) REVERT: A 168 ARG cc_start: 0.7658 (mtp85) cc_final: 0.7378 (mtt-85) REVERT: A 206 ASN cc_start: 0.7974 (m-40) cc_final: 0.7615 (m110) REVERT: A 232 ASN cc_start: 0.7725 (p0) cc_final: 0.7240 (p0) REVERT: A 438 ARG cc_start: 0.7203 (mtm180) cc_final: 0.6005 (tmt170) REVERT: H 46 GLU cc_start: 0.7909 (tp30) cc_final: 0.7326 (tp30) REVERT: H 70 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7665 (mtt) REVERT: H 104 ARG cc_start: 0.8605 (mtm180) cc_final: 0.8378 (mpp-170) REVERT: L 86 TYR cc_start: 0.8276 (m-80) cc_final: 0.7947 (m-80) REVERT: L 102 THR cc_start: 0.8609 (t) cc_final: 0.8374 (t) REVERT: B 112 ASP cc_start: 0.7818 (t0) cc_final: 0.7493 (t0) REVERT: B 154 VAL cc_start: 0.7502 (OUTLIER) cc_final: 0.7178 (t) REVERT: B 251 ASP cc_start: 0.8252 (m-30) cc_final: 0.7998 (m-30) REVERT: B 258 VAL cc_start: 0.8303 (m) cc_final: 0.8050 (t) REVERT: B 259 VAL cc_start: 0.8220 (OUTLIER) cc_final: 0.7875 (t) REVERT: B 278 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.7074 (mtt) REVERT: B 348 VAL cc_start: 0.8378 (OUTLIER) cc_final: 0.8141 (t) outliers start: 32 outliers final: 14 residues processed: 189 average time/residue: 0.3499 time to fit residues: 71.0844 Evaluate side-chains 195 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 66 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN B 340 GLN B 349 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.121652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.110302 restraints weight = 10204.073| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.57 r_work: 0.3337 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7837 Z= 0.190 Angle : 0.632 9.255 10695 Z= 0.320 Chirality : 0.047 0.163 1216 Planarity : 0.004 0.044 1380 Dihedral : 6.589 46.341 1262 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.94 % Allowed : 14.55 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.94 (0.26), residues: 1000 helix: -0.43 (0.52), residues: 98 sheet: -0.01 (0.27), residues: 363 loop : -1.07 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 339 TYR 0.022 0.002 TYR L 50 PHE 0.016 0.002 PHE B 142 TRP 0.018 0.003 TRP A 395 HIS 0.006 0.002 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 7820) covalent geometry : angle 0.62093 (10652) SS BOND : bond 0.00250 ( 8) SS BOND : angle 1.19743 ( 16) hydrogen bonds : bond 0.03556 ( 254) hydrogen bonds : angle 6.30341 ( 669) link_ALPHA1-3 : bond 0.02210 ( 1) link_ALPHA1-3 : angle 2.38665 ( 3) link_ALPHA1-6 : bond 0.01260 ( 1) link_ALPHA1-6 : angle 1.52738 ( 3) link_BETA1-4 : bond 0.00439 ( 2) link_BETA1-4 : angle 2.61415 ( 6) link_NAG-ASN : bond 0.00347 ( 5) link_NAG-ASN : angle 2.32697 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 46 THR cc_start: 0.7970 (t) cc_final: 0.7744 (m) REVERT: A 168 ARG cc_start: 0.7628 (mtp85) cc_final: 0.7275 (mtt-85) REVERT: A 206 ASN cc_start: 0.7977 (m-40) cc_final: 0.7619 (m110) REVERT: A 438 ARG cc_start: 0.7263 (mtm180) cc_final: 0.5949 (tmt170) REVERT: H 46 GLU cc_start: 0.7979 (tp30) cc_final: 0.7373 (tp30) REVERT: H 104 ARG cc_start: 0.8596 (mtm180) cc_final: 0.8390 (mpp-170) REVERT: L 86 TYR cc_start: 0.8294 (m-80) cc_final: 0.7971 (m-80) REVERT: L 102 THR cc_start: 0.8617 (t) cc_final: 0.8385 (t) REVERT: B 112 ASP cc_start: 0.7914 (t0) cc_final: 0.7573 (t0) REVERT: B 154 VAL cc_start: 0.7458 (m) cc_final: 0.7152 (t) REVERT: B 251 ASP cc_start: 0.8286 (m-30) cc_final: 0.8007 (m-30) REVERT: B 258 VAL cc_start: 0.8260 (m) cc_final: 0.8002 (t) REVERT: B 259 VAL cc_start: 0.8181 (OUTLIER) cc_final: 0.7848 (t) REVERT: B 278 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.7085 (mtt) REVERT: B 348 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8140 (t) REVERT: B 391 THR cc_start: 0.8291 (m) cc_final: 0.7785 (p) outliers start: 38 outliers final: 19 residues processed: 187 average time/residue: 0.3659 time to fit residues: 73.1983 Evaluate side-chains 198 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 13 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 73 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 77 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN B 119 ASN B 340 GLN B 349 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.121632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110367 restraints weight = 10214.806| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.56 r_work: 0.3334 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7837 Z= 0.201 Angle : 0.644 9.408 10695 Z= 0.326 Chirality : 0.047 0.150 1216 Planarity : 0.004 0.043 1380 Dihedral : 5.891 45.821 1262 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 5.06 % Allowed : 14.94 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.77 (0.26), residues: 1000 helix: -0.22 (0.53), residues: 98 sheet: 0.06 (0.27), residues: 360 loop : -0.93 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 339 TYR 0.028 0.002 TYR H 32 PHE 0.018 0.002 PHE B 142 TRP 0.017 0.003 TRP A 395 HIS 0.006 0.002 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 7820) covalent geometry : angle 0.63105 (10652) SS BOND : bond 0.00258 ( 8) SS BOND : angle 1.20814 ( 16) hydrogen bonds : bond 0.03540 ( 254) hydrogen bonds : angle 6.23830 ( 669) link_ALPHA1-3 : bond 0.02239 ( 1) link_ALPHA1-3 : angle 2.71859 ( 3) link_ALPHA1-6 : bond 0.01278 ( 1) link_ALPHA1-6 : angle 2.54747 ( 3) link_BETA1-4 : bond 0.00422 ( 2) link_BETA1-4 : angle 2.65431 ( 6) link_NAG-ASN : bond 0.00464 ( 5) link_NAG-ASN : angle 2.40382 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 46 THR cc_start: 0.7958 (t) cc_final: 0.7732 (m) REVERT: A 168 ARG cc_start: 0.7666 (mtp85) cc_final: 0.7459 (mtt-85) REVERT: A 206 ASN cc_start: 0.7985 (m-40) cc_final: 0.7686 (m110) REVERT: A 438 ARG cc_start: 0.7276 (mtm180) cc_final: 0.5965 (tmt170) REVERT: H 46 GLU cc_start: 0.7989 (tp30) cc_final: 0.7246 (tp30) REVERT: L 86 TYR cc_start: 0.8286 (m-80) cc_final: 0.7916 (m-80) REVERT: L 91 SER cc_start: 0.7990 (t) cc_final: 0.7521 (t) REVERT: L 98 PHE cc_start: 0.8376 (m-80) cc_final: 0.7967 (m-80) REVERT: L 102 THR cc_start: 0.8617 (t) cc_final: 0.8393 (t) REVERT: B 203 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7409 (mtmp) REVERT: B 258 VAL cc_start: 0.8248 (m) cc_final: 0.8020 (t) REVERT: B 278 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.7098 (mtt) REVERT: B 348 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8175 (t) REVERT: B 391 THR cc_start: 0.8284 (m) cc_final: 0.7779 (p) outliers start: 39 outliers final: 23 residues processed: 190 average time/residue: 0.3722 time to fit residues: 75.9166 Evaluate side-chains 195 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 356 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN B 349 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.121163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.109988 restraints weight = 10180.690| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.55 r_work: 0.3328 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7837 Z= 0.236 Angle : 0.674 10.196 10695 Z= 0.342 Chirality : 0.048 0.148 1216 Planarity : 0.004 0.047 1380 Dihedral : 5.823 47.855 1262 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.03 % Allowed : 16.23 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.77 (0.26), residues: 1000 helix: -0.30 (0.53), residues: 98 sheet: 0.02 (0.27), residues: 361 loop : -0.88 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 339 TYR 0.026 0.002 TYR A 112 PHE 0.019 0.002 PHE B 142 TRP 0.019 0.003 TRP B 230 HIS 0.007 0.002 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00566 ( 7820) covalent geometry : angle 0.65900 (10652) SS BOND : bond 0.00295 ( 8) SS BOND : angle 1.52357 ( 16) hydrogen bonds : bond 0.03723 ( 254) hydrogen bonds : angle 6.33519 ( 669) link_ALPHA1-3 : bond 0.02102 ( 1) link_ALPHA1-3 : angle 3.00750 ( 3) link_ALPHA1-6 : bond 0.01052 ( 1) link_ALPHA1-6 : angle 2.52560 ( 3) link_BETA1-4 : bond 0.00445 ( 2) link_BETA1-4 : angle 2.74111 ( 6) link_NAG-ASN : bond 0.00481 ( 5) link_NAG-ASN : angle 2.58334 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 46 THR cc_start: 0.7973 (t) cc_final: 0.7747 (m) REVERT: A 168 ARG cc_start: 0.7691 (mtp85) cc_final: 0.7470 (mtt-85) REVERT: A 206 ASN cc_start: 0.7991 (m-40) cc_final: 0.7684 (m110) REVERT: A 391 LEU cc_start: 0.8545 (mt) cc_final: 0.8258 (mp) REVERT: A 438 ARG cc_start: 0.7257 (mtm180) cc_final: 0.5922 (tmt170) REVERT: H 46 GLU cc_start: 0.8000 (tp30) cc_final: 0.7226 (tp30) REVERT: L 86 TYR cc_start: 0.8298 (m-80) cc_final: 0.7842 (m-80) REVERT: L 91 SER cc_start: 0.7983 (t) cc_final: 0.7581 (t) REVERT: L 102 THR cc_start: 0.8685 (t) cc_final: 0.8439 (t) REVERT: B 203 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7421 (mtmp) REVERT: B 258 VAL cc_start: 0.8235 (m) cc_final: 0.8003 (t) REVERT: B 278 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.7105 (mtt) REVERT: B 348 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.8153 (t) REVERT: B 391 THR cc_start: 0.8287 (m) cc_final: 0.7780 (p) outliers start: 31 outliers final: 24 residues processed: 181 average time/residue: 0.3556 time to fit residues: 69.1398 Evaluate side-chains 197 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 75 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.122408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111212 restraints weight = 10216.833| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.56 r_work: 0.3348 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7837 Z= 0.168 Angle : 0.620 10.606 10695 Z= 0.313 Chirality : 0.046 0.151 1216 Planarity : 0.004 0.043 1380 Dihedral : 5.546 46.452 1262 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.29 % Allowed : 16.36 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.63 (0.27), residues: 1000 helix: -0.03 (0.53), residues: 98 sheet: 0.12 (0.27), residues: 360 loop : -0.83 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.022 0.002 TYR H 32 PHE 0.016 0.002 PHE L 98 TRP 0.015 0.002 TRP B 230 HIS 0.005 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 7820) covalent geometry : angle 0.60628 (10652) SS BOND : bond 0.00190 ( 8) SS BOND : angle 1.27918 ( 16) hydrogen bonds : bond 0.03354 ( 254) hydrogen bonds : angle 6.17900 ( 669) link_ALPHA1-3 : bond 0.02279 ( 1) link_ALPHA1-3 : angle 3.47182 ( 3) link_ALPHA1-6 : bond 0.00942 ( 1) link_ALPHA1-6 : angle 2.28281 ( 3) link_BETA1-4 : bond 0.00540 ( 2) link_BETA1-4 : angle 2.44116 ( 6) link_NAG-ASN : bond 0.00266 ( 5) link_NAG-ASN : angle 2.31887 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 46 THR cc_start: 0.7950 (t) cc_final: 0.7726 (m) REVERT: A 206 ASN cc_start: 0.8001 (m-40) cc_final: 0.7715 (m110) REVERT: A 391 LEU cc_start: 0.8513 (mt) cc_final: 0.8251 (mp) REVERT: A 438 ARG cc_start: 0.7305 (mtm180) cc_final: 0.5968 (tmt170) REVERT: H 46 GLU cc_start: 0.7995 (tp30) cc_final: 0.7238 (tp30) REVERT: L 86 TYR cc_start: 0.8274 (m-80) cc_final: 0.7969 (m-80) REVERT: L 91 SER cc_start: 0.7948 (t) cc_final: 0.7548 (t) REVERT: L 98 PHE cc_start: 0.8389 (m-80) cc_final: 0.7970 (m-80) REVERT: L 102 THR cc_start: 0.8645 (t) cc_final: 0.8383 (t) REVERT: B 112 ASP cc_start: 0.7897 (t0) cc_final: 0.7584 (t0) REVERT: B 203 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7432 (mtmp) REVERT: B 278 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.7065 (mtt) REVERT: B 348 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8140 (t) REVERT: B 391 THR cc_start: 0.8274 (m) cc_final: 0.7763 (p) outliers start: 33 outliers final: 24 residues processed: 185 average time/residue: 0.3766 time to fit residues: 74.8888 Evaluate side-chains 196 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- 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: 62.5506 > 50: distance: 19 - 36: 32.559 distance: 23 - 41: 27.687 distance: 29 - 31: 26.108 distance: 31 - 32: 43.360 distance: 32 - 33: 23.947 distance: 32 - 35: 36.688 distance: 33 - 34: 12.528 distance: 33 - 36: 40.822 distance: 37 - 38: 14.924 distance: 37 - 40: 12.133 distance: 38 - 39: 43.450 distance: 38 - 41: 20.868 distance: 41 - 42: 10.470 distance: 42 - 43: 26.059 distance: 42 - 45: 16.724 distance: 43 - 44: 15.616 distance: 43 - 49: 12.310 distance: 44 - 69: 25.305 distance: 45 - 46: 32.221 distance: 46 - 47: 11.278 distance: 46 - 48: 8.548 distance: 49 - 50: 20.836 distance: 50 - 51: 13.104 distance: 50 - 53: 25.477 distance: 51 - 52: 26.985 distance: 51 - 55: 23.760 distance: 55 - 56: 23.349 distance: 56 - 57: 33.282 distance: 56 - 59: 12.310 distance: 57 - 58: 17.976 distance: 57 - 60: 12.922 distance: 60 - 61: 18.415 distance: 61 - 62: 15.382 distance: 61 - 64: 16.439 distance: 62 - 63: 11.578 distance: 62 - 69: 20.312 distance: 64 - 65: 31.342 distance: 65 - 66: 22.652 distance: 66 - 67: 14.300 distance: 67 - 68: 26.760 distance: 69 - 70: 45.961 distance: 70 - 71: 6.496 distance: 70 - 73: 13.775 distance: 71 - 72: 23.600 distance: 71 - 77: 27.024 distance: 73 - 74: 38.885 distance: 74 - 75: 21.046 distance: 75 - 76: 36.453 distance: 77 - 78: 34.539 distance: 78 - 79: 31.323 distance: 78 - 81: 29.872 distance: 79 - 80: 52.458 distance: 79 - 82: 52.999 distance: 82 - 83: 43.942 distance: 83 - 84: 21.631 distance: 83 - 86: 29.770 distance: 84 - 85: 9.057 distance: 84 - 87: 5.390 distance: 87 - 88: 8.616 distance: 88 - 89: 12.771 distance: 88 - 91: 27.627 distance: 89 - 90: 15.379 distance: 89 - 98: 12.116 distance: 92 - 93: 23.865 distance: 92 - 94: 7.457 distance: 93 - 95: 14.003 distance: 94 - 96: 15.373 distance: 95 - 97: 9.351 distance: 96 - 97: 14.782