Starting phenix.real_space_refine on Fri Aug 22 20:17:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sda_40350/08_2025/8sda_40350.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sda_40350/08_2025/8sda_40350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sda_40350/08_2025/8sda_40350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sda_40350/08_2025/8sda_40350.map" model { file = "/net/cci-nas-00/data/ceres_data/8sda_40350/08_2025/8sda_40350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sda_40350/08_2025/8sda_40350.cif" } resolution = 3.32 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= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 7 5.49 5 S 36 5.16 5 C 4963 2.51 5 N 1117 2.21 5 O 1287 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: 7414 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1825 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1823 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1744 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain breaks: 2 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 4, 'PHE:plan': 1, 'ARG:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 76 Chain: "C" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1749 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 2, 'ASP:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 5, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 116 Unusual residues: {' K': 3, 'POV': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-3': 3, 'POV:plan-2': 2} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' K': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 50 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-1': 1, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 1, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 1.58, per 1000 atoms: 0.21 Number of scatterers: 7414 At special positions: 0 Unit cell: (96.28, 96.28, 78.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 36 16.00 P 7 15.00 O 1287 8.00 N 1117 7.00 C 4963 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 282.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1790 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 0 sheets defined 85.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.709A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 206 removed outlier: 4.047A pdb=" N THR A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 247 removed outlier: 3.682A pdb=" N VAL A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 256 removed outlier: 3.569A pdb=" N PHE A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 276 Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 300 through 308 Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 323 through 350 Processing helix chain 'A' and resid 359 through 373 removed outlier: 4.173A pdb=" N TRP A 365 " --> pdb=" O PRO A 361 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TRP A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 403 removed outlier: 3.694A pdb=" N ILE A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 428 removed outlier: 3.567A pdb=" N ILE A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 removed outlier: 3.521A pdb=" N LYS B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 205 Processing helix chain 'B' and resid 224 through 247 Processing helix chain 'B' and resid 250 through 256 removed outlier: 3.560A pdb=" N PHE B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 276 Proline residue: B 268 - end of helix Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 300 through 308 Processing helix chain 'B' and resid 310 through 323 Processing helix chain 'B' and resid 323 through 349 removed outlier: 3.520A pdb=" N LEU B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 372 removed outlier: 4.157A pdb=" N TRP B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TRP B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 400 Processing helix chain 'B' and resid 404 through 428 removed outlier: 3.735A pdb=" N PHE B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 181 through 206 removed outlier: 4.002A pdb=" N THR D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 229 Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 250 through 256 removed outlier: 3.596A pdb=" N GLY D 256 " --> pdb=" O LYS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 275 Proline residue: D 268 - end of helix Processing helix chain 'D' and resid 289 through 299 Processing helix chain 'D' and resid 300 through 308 Processing helix chain 'D' and resid 310 through 349 removed outlier: 4.220A pdb=" N ARG D 321 " --> pdb=" O GLY D 317 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN D 325 " --> pdb=" O ARG D 321 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLU D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU D 329 " --> pdb=" O ASN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 372 removed outlier: 4.113A pdb=" N TRP D 365 " --> pdb=" O PRO D 361 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TRP D 366 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 403 removed outlier: 3.692A pdb=" N ALA D 402 " --> pdb=" O VAL D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 427 removed outlier: 4.368A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER D 413 " --> pdb=" O VAL D 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 205 Processing helix chain 'C' and resid 224 through 247 removed outlier: 3.858A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 247 " --> pdb=" O ARG C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 256 removed outlier: 4.013A pdb=" N PHE C 254 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY C 256 " --> pdb=" O LYS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 276 removed outlier: 3.740A pdb=" N ILE C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Proline residue: C 268 - end of helix Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 300 through 308 Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.524A pdb=" N GLN C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 349 removed outlier: 3.585A pdb=" N GLY C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 372 removed outlier: 4.116A pdb=" N TRP C 365 " --> pdb=" O PRO C 361 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TRP C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C 372 " --> pdb=" O THR C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 403 Processing helix chain 'C' and resid 403 through 427 removed outlier: 4.594A pdb=" N ILE C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER C 413 " --> pdb=" O VAL C 409 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1635 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: 1.10 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1107 1.30 - 1.43: 1874 1.43 - 1.56: 4478 1.56 - 1.68: 26 1.68 - 1.81: 65 Bond restraints: 7550 Sorted by residual: bond pdb=" C21 POV D 602 " pdb=" O21 POV D 602 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" C21 POV A 603 " pdb=" O21 POV A 603 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C21 POV A 604 " pdb=" O21 POV A 604 " ideal model delta sigma weight residual 1.330 1.457 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C31 POV A 606 " pdb=" O31 POV A 606 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C21 POV C 603 " pdb=" O21 POV C 603 " ideal model delta sigma weight residual 1.330 1.444 -0.114 2.00e-02 2.50e+03 3.27e+01 ... (remaining 7545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 9903 2.55 - 5.11: 218 5.11 - 7.66: 67 7.66 - 10.22: 32 10.22 - 12.77: 15 Bond angle restraints: 10235 Sorted by residual: angle pdb=" O13 POV A 601 " pdb=" P POV A 601 " pdb=" O14 POV A 601 " ideal model delta sigma weight residual 121.11 108.34 12.77 3.00e+00 1.11e-01 1.81e+01 angle pdb=" O11 POV A 602 " pdb=" P POV A 602 " pdb=" O12 POV A 602 " ideal model delta sigma weight residual 97.67 109.76 -12.09 3.00e+00 1.11e-01 1.62e+01 angle pdb=" O13 POV B 602 " pdb=" P POV B 602 " pdb=" O14 POV B 602 " ideal model delta sigma weight residual 121.11 109.07 12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" O11 POV D 601 " pdb=" P POV D 601 " pdb=" O12 POV D 601 " ideal model delta sigma weight residual 97.67 109.48 -11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" O11 POV C 602 " pdb=" P POV C 602 " pdb=" O12 POV C 602 " ideal model delta sigma weight residual 97.67 109.43 -11.76 3.00e+00 1.11e-01 1.54e+01 ... (remaining 10230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.14: 4212 26.14 - 52.27: 221 52.27 - 78.41: 33 78.41 - 104.54: 9 104.54 - 130.68: 1 Dihedral angle restraints: 4476 sinusoidal: 1731 harmonic: 2745 Sorted by residual: dihedral pdb=" C3 POV A 601 " pdb=" C31 POV A 601 " pdb=" O31 POV A 601 " pdb=" C32 POV A 601 " ideal model delta sinusoidal sigma weight residual 172.61 41.93 130.68 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" CB GLU A 239 " pdb=" CG GLU A 239 " pdb=" CD GLU A 239 " pdb=" OE1 GLU A 239 " ideal model delta sinusoidal sigma weight residual 0.00 -83.23 83.23 1 3.00e+01 1.11e-03 9.41e+00 dihedral pdb=" CA GLU B 349 " pdb=" CB GLU B 349 " pdb=" CG GLU B 349 " pdb=" CD GLU B 349 " ideal model delta sinusoidal sigma weight residual 60.00 115.59 -55.59 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 4473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 996 0.051 - 0.103: 215 0.103 - 0.154: 27 0.154 - 0.205: 5 0.205 - 0.257: 2 Chirality restraints: 1245 Sorted by residual: chirality pdb=" CG LEU D 327 " pdb=" CB LEU D 327 " pdb=" CD1 LEU D 327 " pdb=" CD2 LEU D 327 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA LEU C 225 " pdb=" N LEU C 225 " pdb=" C LEU C 225 " pdb=" CB LEU C 225 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA HIS C 227 " pdb=" N HIS C 227 " pdb=" C HIS C 227 " pdb=" CB HIS C 227 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.90e-01 ... (remaining 1242 not shown) Planarity restraints: 1217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 406 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C PRO B 406 " -0.056 2.00e-02 2.50e+03 pdb=" O PRO B 406 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE B 407 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 397 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.14e+00 pdb=" C GLY D 397 " 0.052 2.00e-02 2.50e+03 pdb=" O GLY D 397 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL D 398 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 207 " -0.030 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A 208 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " -0.025 5.00e-02 4.00e+02 ... (remaining 1214 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.81: 2086 2.81 - 3.39: 9155 3.39 - 3.97: 13853 3.97 - 4.56: 19809 4.56 - 5.14: 27639 Nonbonded interactions: 72542 Sorted by model distance: nonbonded pdb=" O THR B 319 " pdb=" OG SER B 323 " model vdw 2.225 3.040 nonbonded pdb=" O ILE D 407 " pdb=" ND2 ASN D 411 " model vdw 2.280 3.120 nonbonded pdb=" O TYR A 376 " pdb=" K K A 609 " model vdw 2.320 2.850 nonbonded pdb=" O THR C 372 " pdb=" OG1 THR C 373 " model vdw 2.327 3.040 nonbonded pdb=" O THR A 372 " pdb=" OG1 THR A 373 " model vdw 2.355 3.040 ... (remaining 72537 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 172 through 173 and (name N or name CA or name C or name \ O or name CB )) or resid 174 through 211 or resid 224 through 228 or (resid 229 \ through 230 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 1 through 250 or (resid 251 through 252 and (name N or name CA or name C or name \ O or name CB )) or resid 253 through 273 or (resid 274 and (name N or name CA o \ r name C or name O or name CB )) or resid 275 or resid 288 through 308 or (resid \ 309 and (name N or name CA or name C or name O or name CB )) or resid 310 throu \ gh 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) or \ resid 319 through 321 or (resid 322 and (name N or name CA or name C or name O \ or name CB )) or resid 323 through 409 or (resid 410 and (name N or name CA or n \ ame C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 416 or (resid \ 417 and (name N or name CA or name C or name O or name CB )) or resid 418 throu \ gh 419 or (resid 420 through 427 and (name N or name CA or name C or name O or n \ ame CB )))) selection = (chain 'B' and ((resid 172 through 173 and (name N or name CA or name C or name \ O or name CB )) or resid 174 through 211 or resid 224 through 228 or (resid 229 \ through 230 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 1 through 250 or (resid 251 through 252 and (name N or name CA or name C or name \ O or name CB )) or resid 253 through 273 or (resid 274 and (name N or name CA o \ r name C or name O or name CB )) or resid 275 or resid 288 through 308 or (resid \ 309 and (name N or name CA or name C or name O or name CB )) or resid 310 throu \ gh 321 or (resid 322 and (name N or name CA or name C or name O or name CB )) or \ resid 323 through 325 or (resid 326 and (name N or name CA or name C or name O \ or name CB )) or resid 327 through 409 or (resid 410 and (name N or name CA or n \ ame C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 416 or (resid \ 417 and (name N or name CA or name C or name O or name CB )) or resid 418 throu \ gh 419 or (resid 420 through 427 and (name N or name CA or name C or name O or n \ ame CB )))) selection = (chain 'C' and (resid 172 through 211 or resid 224 through 228 or (resid 229 thr \ ough 230 and (name N or name CA or name C or name O or name CB )) or resid 231 t \ hrough 273 or (resid 274 and (name N or name CA or name C or name O or name CB ) \ ) or resid 275 or resid 288 through 409 or (resid 410 and (name N or name CA or \ name C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name \ N or name CA or name C or name O or name CB )) or resid 415 through 427)) selection = (chain 'D' and ((resid 172 through 173 and (name N or name CA or name C or name \ O or name CB )) or resid 174 through 175 or (resid 176 through 177 and (name N o \ r name CA or name C or name O or name CB )) or resid 178 through 308 or (resid 3 \ 09 and (name N or name CA or name C or name O or name CB )) or resid 310 through \ 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) or r \ esid 319 through 427)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.610 Find NCS groups from input model: 0.180 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 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 : 0.008 0.128 7550 Z= 0.425 Angle : 1.113 12.774 10235 Z= 0.501 Chirality : 0.043 0.257 1245 Planarity : 0.005 0.045 1217 Dihedral : 15.987 130.675 2686 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: 1.62 (0.29), residues: 915 helix: 1.30 (0.20), residues: 740 sheet: None (None), residues: 0 loop : 0.42 (0.53), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 296 TYR 0.017 0.001 TYR C 416 PHE 0.011 0.001 PHE A 194 TRP 0.009 0.001 TRP A 172 HIS 0.004 0.001 HIS C 227 Details of bonding type rmsd covalent geometry : bond 0.00795 ( 7550) covalent geometry : angle 1.11287 (10235) hydrogen bonds : bond 0.15137 ( 569) hydrogen bonds : angle 5.78705 ( 1635) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.273 Fit side-chains REVERT: D 298 MET cc_start: 0.7594 (ttm) cc_final: 0.6911 (tmm) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1054 time to fit residues: 23.4595 Evaluate side-chains 123 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 309 HIS D 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.157695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123353 restraints weight = 10019.176| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.97 r_work: 0.3272 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7550 Z= 0.144 Angle : 0.570 7.800 10235 Z= 0.290 Chirality : 0.039 0.141 1245 Planarity : 0.004 0.032 1217 Dihedral : 13.133 108.629 1160 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.04 % Allowed : 10.85 % Favored : 87.11 % 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: 2.36 (0.29), residues: 915 helix: 1.84 (0.19), residues: 758 sheet: None (None), residues: 0 loop : 0.41 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 308 TYR 0.018 0.001 TYR D 269 PHE 0.021 0.001 PHE B 415 TRP 0.010 0.001 TRP B 251 HIS 0.002 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7550) covalent geometry : angle 0.56967 (10235) hydrogen bonds : bond 0.04014 ( 569) hydrogen bonds : angle 4.03609 ( 1635) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.288 Fit side-chains REVERT: A 418 GLU cc_start: 0.8438 (tp30) cc_final: 0.8012 (tp30) REVERT: B 322 ARG cc_start: 0.8345 (tmm-80) cc_final: 0.8043 (ttp80) REVERT: D 238 MET cc_start: 0.6542 (ttp) cc_final: 0.6197 (tmm) REVERT: D 298 MET cc_start: 0.7827 (ttm) cc_final: 0.7061 (tmm) outliers start: 15 outliers final: 9 residues processed: 164 average time/residue: 0.0968 time to fit residues: 20.4726 Evaluate side-chains 141 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 398 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 65 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.156737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123960 restraints weight = 10100.088| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.03 r_work: 0.3250 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7550 Z= 0.134 Angle : 0.523 6.675 10235 Z= 0.265 Chirality : 0.039 0.131 1245 Planarity : 0.004 0.040 1217 Dihedral : 11.848 99.505 1160 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.44 % Allowed : 13.16 % Favored : 84.40 % 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: 2.60 (0.28), residues: 915 helix: 2.02 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.50 (0.49), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 322 TYR 0.012 0.001 TYR B 269 PHE 0.011 0.001 PHE A 346 TRP 0.007 0.001 TRP B 366 HIS 0.002 0.000 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7550) covalent geometry : angle 0.52259 (10235) hydrogen bonds : bond 0.03514 ( 569) hydrogen bonds : angle 3.76196 ( 1635) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.263 Fit side-chains REVERT: A 418 GLU cc_start: 0.8502 (tp30) cc_final: 0.8214 (tp30) REVERT: B 322 ARG cc_start: 0.8441 (tmm-80) cc_final: 0.8143 (ttp80) REVERT: D 238 MET cc_start: 0.6590 (ttp) cc_final: 0.6216 (tmm) REVERT: D 298 MET cc_start: 0.7795 (ttm) cc_final: 0.7038 (tmm) outliers start: 18 outliers final: 9 residues processed: 153 average time/residue: 0.1021 time to fit residues: 20.1851 Evaluate side-chains 140 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 56 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.155974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.122377 restraints weight = 10255.383| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.13 r_work: 0.3225 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7550 Z= 0.131 Angle : 0.515 6.752 10235 Z= 0.260 Chirality : 0.038 0.128 1245 Planarity : 0.004 0.035 1217 Dihedral : 11.037 87.522 1160 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.31 % Allowed : 15.88 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.70 (0.29), residues: 915 helix: 2.07 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 0.56 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 296 TYR 0.012 0.001 TYR B 269 PHE 0.018 0.001 PHE B 274 TRP 0.007 0.001 TRP A 365 HIS 0.002 0.000 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7550) covalent geometry : angle 0.51516 (10235) hydrogen bonds : bond 0.03295 ( 569) hydrogen bonds : angle 3.66000 ( 1635) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.264 Fit side-chains REVERT: A 418 GLU cc_start: 0.8619 (tp30) cc_final: 0.8274 (tp30) REVERT: A 423 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7718 (tm-30) REVERT: B 322 ARG cc_start: 0.8429 (tmm-80) cc_final: 0.8157 (ttm-80) REVERT: B 343 SER cc_start: 0.8775 (t) cc_final: 0.8571 (m) REVERT: B 372 THR cc_start: 0.9356 (OUTLIER) cc_final: 0.9129 (p) REVERT: D 238 MET cc_start: 0.6723 (ttp) cc_final: 0.6273 (tmm) REVERT: D 298 MET cc_start: 0.7816 (ttm) cc_final: 0.7069 (tmm) REVERT: C 185 LYS cc_start: 0.7915 (tptm) cc_final: 0.7691 (tptt) REVERT: C 238 MET cc_start: 0.7053 (tmm) cc_final: 0.6809 (tmm) outliers start: 17 outliers final: 10 residues processed: 150 average time/residue: 0.1120 time to fit residues: 21.5863 Evaluate side-chains 146 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 85 optimal weight: 0.0570 chunk 68 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 54 optimal weight: 0.0970 chunk 23 optimal weight: 8.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.157592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.124273 restraints weight = 10242.722| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.20 r_work: 0.3245 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7550 Z= 0.112 Angle : 0.494 6.793 10235 Z= 0.248 Chirality : 0.037 0.123 1245 Planarity : 0.004 0.035 1217 Dihedral : 10.525 84.340 1160 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.31 % Allowed : 17.23 % Favored : 80.46 % 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: 2.90 (0.29), residues: 915 helix: 2.21 (0.19), residues: 751 sheet: None (None), residues: 0 loop : 0.68 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 296 TYR 0.010 0.001 TYR B 269 PHE 0.018 0.001 PHE B 274 TRP 0.006 0.001 TRP D 365 HIS 0.001 0.000 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7550) covalent geometry : angle 0.49388 (10235) hydrogen bonds : bond 0.03098 ( 569) hydrogen bonds : angle 3.54413 ( 1635) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.258 Fit side-chains REVERT: A 418 GLU cc_start: 0.8642 (tp30) cc_final: 0.8275 (tp30) REVERT: A 422 GLN cc_start: 0.8145 (mm110) cc_final: 0.7822 (mm110) REVERT: A 423 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7726 (tm-30) REVERT: B 309 HIS cc_start: 0.8844 (m90) cc_final: 0.8628 (m90) REVERT: B 322 ARG cc_start: 0.8368 (tmm-80) cc_final: 0.8154 (ttm-80) REVERT: B 372 THR cc_start: 0.9322 (OUTLIER) cc_final: 0.9097 (p) REVERT: D 238 MET cc_start: 0.6795 (ttp) cc_final: 0.6555 (tmm) REVERT: D 298 MET cc_start: 0.7803 (ttm) cc_final: 0.7111 (tmm) REVERT: C 185 LYS cc_start: 0.7933 (tptm) cc_final: 0.7707 (tptt) REVERT: C 238 MET cc_start: 0.7050 (tmm) cc_final: 0.6814 (tmm) REVERT: C 297 ILE cc_start: 0.8563 (mt) cc_final: 0.8195 (mt) outliers start: 17 outliers final: 11 residues processed: 149 average time/residue: 0.0896 time to fit residues: 17.3076 Evaluate side-chains 147 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.155563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.122163 restraints weight = 10125.189| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.16 r_work: 0.3211 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7550 Z= 0.133 Angle : 0.521 7.828 10235 Z= 0.260 Chirality : 0.038 0.127 1245 Planarity : 0.004 0.035 1217 Dihedral : 10.356 84.460 1160 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.31 % Allowed : 18.18 % Favored : 79.51 % 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: 2.86 (0.29), residues: 915 helix: 2.18 (0.19), residues: 757 sheet: None (None), residues: 0 loop : 0.63 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 296 TYR 0.010 0.001 TYR B 269 PHE 0.020 0.001 PHE B 274 TRP 0.006 0.001 TRP B 366 HIS 0.002 0.000 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7550) covalent geometry : angle 0.52118 (10235) hydrogen bonds : bond 0.03175 ( 569) hydrogen bonds : angle 3.55568 ( 1635) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.224 Fit side-chains REVERT: A 418 GLU cc_start: 0.8655 (tp30) cc_final: 0.8251 (tp30) REVERT: A 422 GLN cc_start: 0.8164 (mm110) cc_final: 0.7818 (mm110) REVERT: A 423 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7709 (tm-30) REVERT: B 309 HIS cc_start: 0.8851 (m90) cc_final: 0.8609 (m90) REVERT: B 372 THR cc_start: 0.9358 (OUTLIER) cc_final: 0.9134 (p) REVERT: D 238 MET cc_start: 0.6864 (ttp) cc_final: 0.6590 (tmm) REVERT: D 298 MET cc_start: 0.7826 (ttm) cc_final: 0.7150 (tmm) REVERT: C 185 LYS cc_start: 0.7953 (tptm) cc_final: 0.7734 (tptt) REVERT: C 238 MET cc_start: 0.7117 (tmm) cc_final: 0.6885 (tmm) REVERT: C 297 ILE cc_start: 0.8539 (mt) cc_final: 0.8182 (mt) REVERT: C 416 TYR cc_start: 0.7640 (t80) cc_final: 0.7333 (m-80) outliers start: 17 outliers final: 10 residues processed: 143 average time/residue: 0.0957 time to fit residues: 17.8458 Evaluate side-chains 143 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 89 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 0.1980 chunk 62 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 50 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.159202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.124303 restraints weight = 10150.974| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.12 r_work: 0.3247 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7550 Z= 0.111 Angle : 0.505 7.100 10235 Z= 0.252 Chirality : 0.037 0.123 1245 Planarity : 0.004 0.035 1217 Dihedral : 10.055 86.549 1160 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.90 % Allowed : 18.45 % Favored : 79.65 % 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: 2.99 (0.28), residues: 915 helix: 2.26 (0.19), residues: 757 sheet: None (None), residues: 0 loop : 0.72 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 296 TYR 0.009 0.001 TYR B 269 PHE 0.022 0.001 PHE B 274 TRP 0.006 0.001 TRP B 365 HIS 0.001 0.000 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7550) covalent geometry : angle 0.50516 (10235) hydrogen bonds : bond 0.03022 ( 569) hydrogen bonds : angle 3.47934 ( 1635) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.176 Fit side-chains REVERT: A 318 PHE cc_start: 0.8140 (t80) cc_final: 0.7877 (m-80) REVERT: A 418 GLU cc_start: 0.8657 (tp30) cc_final: 0.8221 (tp30) REVERT: A 422 GLN cc_start: 0.8212 (mm110) cc_final: 0.7890 (mm110) REVERT: A 423 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7704 (tm-30) REVERT: B 309 HIS cc_start: 0.8827 (m90) cc_final: 0.8596 (m90) REVERT: B 372 THR cc_start: 0.9332 (OUTLIER) cc_final: 0.9105 (p) REVERT: D 238 MET cc_start: 0.6778 (ttp) cc_final: 0.6483 (tmm) REVERT: D 298 MET cc_start: 0.7893 (ttm) cc_final: 0.7172 (tmm) REVERT: C 238 MET cc_start: 0.7081 (tmm) cc_final: 0.6862 (tmm) REVERT: C 297 ILE cc_start: 0.8537 (mt) cc_final: 0.8198 (mt) REVERT: C 352 GLU cc_start: 0.8005 (pp20) cc_final: 0.7557 (pp20) REVERT: C 416 TYR cc_start: 0.7627 (t80) cc_final: 0.7306 (m-80) outliers start: 14 outliers final: 10 residues processed: 152 average time/residue: 0.0882 time to fit residues: 17.3422 Evaluate side-chains 143 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 262 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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: 56.3841 > 50: distance: 85 - 100: 8.773 distance: 89 - 106: 7.943 distance: 93 - 112: 12.136 distance: 96 - 100: 7.518 distance: 97 - 120: 14.687 distance: 101 - 102: 5.494 distance: 101 - 104: 7.828 distance: 102 - 103: 5.059 distance: 102 - 106: 11.702 distance: 103 - 125: 22.787 distance: 104 - 105: 15.586 distance: 107 - 108: 5.944 distance: 107 - 110: 9.243 distance: 108 - 109: 5.318 distance: 108 - 112: 7.267 distance: 109 - 129: 6.409 distance: 110 - 111: 11.475 distance: 112 - 113: 3.801 distance: 113 - 114: 4.660 distance: 113 - 116: 4.541 distance: 114 - 115: 4.221 distance: 114 - 120: 5.916 distance: 115 - 136: 20.700 distance: 116 - 117: 5.260 distance: 116 - 118: 3.166 distance: 117 - 119: 4.656 distance: 120 - 121: 5.674 distance: 121 - 122: 8.378 distance: 121 - 124: 15.888 distance: 122 - 123: 6.244 distance: 122 - 125: 4.598 distance: 123 - 144: 47.421 distance: 125 - 126: 9.538 distance: 126 - 127: 13.895 distance: 127 - 128: 15.657 distance: 127 - 129: 15.455 distance: 128 - 151: 34.015 distance: 129 - 130: 7.113 distance: 130 - 131: 19.154 distance: 130 - 133: 12.422 distance: 131 - 132: 13.016 distance: 131 - 136: 15.525 distance: 132 - 159: 36.889 distance: 133 - 134: 19.875 distance: 133 - 135: 17.946 distance: 136 - 137: 11.177 distance: 137 - 138: 18.286 distance: 137 - 140: 11.160 distance: 138 - 139: 4.626 distance: 138 - 144: 28.467 distance: 139 - 164: 21.426 distance: 140 - 141: 16.465 distance: 141 - 142: 31.595 distance: 141 - 143: 8.588 distance: 144 - 145: 6.119 distance: 145 - 146: 18.136 distance: 145 - 148: 25.523 distance: 146 - 147: 26.190 distance: 146 - 151: 20.603 distance: 148 - 149: 21.061 distance: 148 - 150: 24.513 distance: 151 - 152: 9.590 distance: 152 - 153: 21.987 distance: 152 - 155: 8.643 distance: 153 - 154: 19.554 distance: 153 - 159: 36.417 distance: 155 - 156: 8.546 distance: 155 - 157: 10.938 distance: 156 - 158: 12.358 distance: 159 - 160: 9.520 distance: 160 - 161: 18.568 distance: 160 - 163: 12.762 distance: 161 - 162: 19.952 distance: 161 - 164: 10.752