Starting phenix.real_space_refine on Thu Sep 26 16:47:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkt_25981/09_2024/7tkt_25981.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkt_25981/09_2024/7tkt_25981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkt_25981/09_2024/7tkt_25981.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkt_25981/09_2024/7tkt_25981.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkt_25981/09_2024/7tkt_25981.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkt_25981/09_2024/7tkt_25981.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 28 5.16 5 C 8844 2.51 5 N 2080 2.21 5 O 2288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13252 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3103 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 23, 'TRANS': 366} Chain breaks: 1 Chain: "D" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3103 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 23, 'TRANS': 366} Chain breaks: 1 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 210 Unusual residues: {'PGW': 13} Classifications: {'RNA': 1, 'undetermined': 13} Modifications used: {'rna3p': 1} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 475 Unresolved non-hydrogen angles: 552 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PGW:plan-1': 11, 'PGW:plan-2': 11, 'PGW:plan-3': 10} Unresolved non-hydrogen planarities: 104 Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 210 Unusual residues: {'PGW': 13} Classifications: {'RNA': 1, 'undetermined': 13} Modifications used: {'rna3p': 1} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 475 Unresolved non-hydrogen angles: 552 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PGW:plan-1': 11, 'PGW:plan-2': 11, 'PGW:plan-3': 10} Unresolved non-hydrogen planarities: 104 Restraints were copied for chains: B, C Time building chain proxies: 8.49, per 1000 atoms: 0.64 Number of scatterers: 13252 At special positions: 0 Unit cell: (105.226, 105.226, 122.763, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 12 15.00 O 2288 8.00 N 2080 7.00 C 8844 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: 3.07 Conformation dependent library (CDL) restraints added in 1.6 seconds 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 63.3% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 12 through 36 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 81 through 89 removed outlier: 4.009A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 112 removed outlier: 4.113A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 107 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 110 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.775A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 158 Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 224 Processing helix chain 'A' and resid 227 through 246 removed outlier: 3.555A pdb=" N ARG A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 268 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 306 through 315 removed outlier: 4.108A pdb=" N ILE A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 404 through 416 removed outlier: 3.855A pdb=" N LEU A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL A 416 " --> pdb=" O GLN A 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 36 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 44 through 56 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 81 through 89 removed outlier: 4.009A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 removed outlier: 4.113A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 107 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 108 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 110 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.775A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 158 Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 224 Processing helix chain 'B' and resid 227 through 246 removed outlier: 3.555A pdb=" N ARG B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 268 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 280 through 292 Processing helix chain 'B' and resid 306 through 315 removed outlier: 4.109A pdb=" N ILE B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 404 through 416 removed outlier: 3.855A pdb=" N LEU B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL B 416 " --> pdb=" O GLN B 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 36 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 81 through 89 removed outlier: 4.010A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 112 removed outlier: 4.113A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 107 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER C 108 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 110 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.775A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 158 Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 224 Processing helix chain 'C' and resid 227 through 246 removed outlier: 3.555A pdb=" N ARG C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 268 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 280 through 292 Processing helix chain 'C' and resid 306 through 315 removed outlier: 4.107A pdb=" N ILE C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 402 Processing helix chain 'C' and resid 404 through 416 removed outlier: 3.855A pdb=" N LEU C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL C 416 " --> pdb=" O GLN C 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 36 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 44 through 56 Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 81 through 89 removed outlier: 4.009A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 112 removed outlier: 4.113A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D 107 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL D 110 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 126 removed outlier: 3.776A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 158 Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 224 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.555A pdb=" N ARG D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 268 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 306 through 315 removed outlier: 4.107A pdb=" N ILE D 310 " --> pdb=" O GLY D 306 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 404 through 416 removed outlier: 3.855A pdb=" N LEU D 414 " --> pdb=" O GLN D 410 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL D 416 " --> pdb=" O GLN D 412 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 6.747A pdb=" N TYR A 327 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA A 383 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 358 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 318 through 319 Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 6.747A pdb=" N TYR B 327 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA B 383 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 358 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 6.747A pdb=" N TYR C 327 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA C 383 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA C 358 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 319 Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 6.747A pdb=" N TYR D 327 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA D 383 " --> pdb=" O TYR D 327 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA D 358 " --> pdb=" O VAL D 348 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 2088 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: 3.86 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3845 1.34 - 1.45: 1694 1.45 - 1.57: 7881 1.57 - 1.69: 16 1.69 - 1.81: 56 Bond restraints: 13492 Sorted by residual: bond pdb=" C10 PGW B 513 " pdb=" C9 PGW B 513 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.33e+01 bond pdb=" C10 PGW D 502 " pdb=" C9 PGW D 502 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" C10 PGW B 510 " pdb=" C9 PGW B 510 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" C10 PGW C 510 " pdb=" C9 PGW C 510 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" C10 PGW A 510 " pdb=" C9 PGW A 510 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.29e+01 ... (remaining 13487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.21: 17753 4.21 - 8.43: 379 8.43 - 12.64: 8 12.64 - 16.86: 0 16.86 - 21.07: 16 Bond angle restraints: 18156 Sorted by residual: angle pdb=" C10 PGW B 513 " pdb=" C9 PGW B 513 " pdb=" C8 PGW B 513 " ideal model delta sigma weight residual 127.02 105.95 21.07 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C10 PGW D 505 " pdb=" C9 PGW D 505 " pdb=" C8 PGW D 505 " ideal model delta sigma weight residual 127.02 105.96 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C10 PGW C 513 " pdb=" C9 PGW C 513 " pdb=" C8 PGW C 513 " ideal model delta sigma weight residual 127.02 105.96 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C10 PGW A 513 " pdb=" C9 PGW A 513 " pdb=" C8 PGW A 513 " ideal model delta sigma weight residual 127.02 105.96 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C10 PGW C 510 " pdb=" C9 PGW C 510 " pdb=" C8 PGW C 510 " ideal model delta sigma weight residual 127.02 106.26 20.76 3.00e+00 1.11e-01 4.79e+01 ... (remaining 18151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 7972 34.68 - 69.36: 208 69.36 - 104.04: 52 104.04 - 138.71: 12 138.71 - 173.39: 32 Dihedral angle restraints: 8276 sinusoidal: 3688 harmonic: 4588 Sorted by residual: dihedral pdb=" C3' CMP C 501 " pdb=" O3' CMP C 501 " pdb=" P CMP C 501 " pdb=" O1P CMP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 100.95 -160.95 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C3' CMP D 507 " pdb=" O3' CMP D 507 " pdb=" P CMP D 507 " pdb=" O1P CMP D 507 " ideal model delta sinusoidal sigma weight residual -60.00 100.94 -160.94 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C3' CMP A 501 " pdb=" O3' CMP A 501 " pdb=" P CMP A 501 " pdb=" O1P CMP A 501 " ideal model delta sinusoidal sigma weight residual -60.00 100.94 -160.94 1 2.00e+01 2.50e-03 4.67e+01 ... (remaining 8273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1311 0.034 - 0.069: 547 0.069 - 0.103: 191 0.103 - 0.137: 39 0.137 - 0.171: 12 Chirality restraints: 2100 Sorted by residual: chirality pdb=" C02 PGW C 503 " pdb=" C01 PGW C 503 " pdb=" C03 PGW C 503 " pdb=" O01 PGW C 503 " both_signs ideal model delta sigma weight residual False 2.36 2.53 -0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" C02 PGW D 509 " pdb=" C01 PGW D 509 " pdb=" C03 PGW D 509 " pdb=" O01 PGW D 509 " both_signs ideal model delta sigma weight residual False 2.36 2.53 -0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CA GLN D 412 " pdb=" N GLN D 412 " pdb=" C GLN D 412 " pdb=" CB GLN D 412 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 2097 not shown) Planarity restraints: 2172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 513 " -0.159 2.00e-02 2.50e+03 1.59e-01 2.52e+02 pdb=" C10 PGW B 513 " 0.161 2.00e-02 2.50e+03 pdb=" C8 PGW B 513 " -0.158 2.00e-02 2.50e+03 pdb=" C9 PGW B 513 " 0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 505 " 0.159 2.00e-02 2.50e+03 1.59e-01 2.52e+02 pdb=" C10 PGW D 505 " -0.161 2.00e-02 2.50e+03 pdb=" C8 PGW D 505 " 0.158 2.00e-02 2.50e+03 pdb=" C9 PGW D 505 " -0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW C 513 " 0.159 2.00e-02 2.50e+03 1.59e-01 2.52e+02 pdb=" C10 PGW C 513 " -0.161 2.00e-02 2.50e+03 pdb=" C8 PGW C 513 " 0.158 2.00e-02 2.50e+03 pdb=" C9 PGW C 513 " -0.156 2.00e-02 2.50e+03 ... (remaining 2169 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1950 2.76 - 3.29: 12129 3.29 - 3.83: 21391 3.83 - 4.36: 22528 4.36 - 4.90: 40837 Nonbonded interactions: 98835 Sorted by model distance: nonbonded pdb=" OG1 THR A 180 " pdb=" OH TYR D 186 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR A 186 " pdb=" OG1 THR B 180 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR B 186 " pdb=" OG1 THR C 180 " model vdw 2.230 3.040 nonbonded pdb=" OH TYR C 186 " pdb=" OG1 THR D 180 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR B 262 " pdb=" OD2 ASP B 388 " model vdw 2.264 3.040 ... (remaining 98830 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 10 through 416 or (resid 502 and (name C06 or name C07 or \ name C08 or name C09 or name C1 or name C10 or name C11 or name C12 or name C2 o \ r name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) o \ r resid 504 through 505 or resid 508 through 509 or (resid 510 through 511 and ( \ name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 513 \ through 514 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 \ )))) selection = (chain 'B' and (resid 10 through 416 or (resid 502 and (name C06 or name C07 or \ name C08 or name C09 or name C1 or name C10 or name C11 or name C12 or name C2 o \ r name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) o \ r resid 504 through 505 or resid 508 through 509 or (resid 510 through 511 and ( \ name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 513 \ through 514 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 \ )))) selection = (chain 'C' and (resid 10 through 416 or (resid 502 and (name C06 or name C07 or \ name C08 or name C09 or name C1 or name C10 or name C11 or name C12 or name C2 o \ r name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) o \ r resid 504 through 505 or resid 508 through 509 or (resid 510 through 511 and ( \ name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 513 \ through 514 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 \ )))) selection = (chain 'D' and (resid 10 through 416 or resid 502 or (resid 504 through 505 and \ (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 508 \ and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resi \ d 509 and (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27 or name C28)) or resid 510 through 511 or resid 513 through 514)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.940 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 0.007 0.171 13492 Z= 0.429 Angle : 1.264 21.069 18156 Z= 0.478 Chirality : 0.044 0.171 2100 Planarity : 0.008 0.159 2172 Dihedral : 21.053 173.393 5316 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.22), residues: 1544 helix: 1.56 (0.18), residues: 936 sheet: 0.59 (0.57), residues: 84 loop : -1.78 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 264 HIS 0.002 0.001 HIS C 292 PHE 0.005 0.001 PHE D 386 TYR 0.009 0.001 TYR B 26 ARG 0.001 0.000 ARG D 311 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.504 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2526 time to fit residues: 56.0754 Evaluate side-chains 125 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 217 ASN C 217 ASN D 217 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13492 Z= 0.196 Angle : 0.620 9.100 18156 Z= 0.289 Chirality : 0.041 0.132 2100 Planarity : 0.004 0.042 2172 Dihedral : 21.069 163.069 2372 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.30 % Allowed : 7.61 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.23), residues: 1544 helix: 1.93 (0.18), residues: 928 sheet: -0.65 (0.41), residues: 156 loop : -1.94 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 176 HIS 0.003 0.001 HIS A 149 PHE 0.012 0.001 PHE D 40 TYR 0.013 0.001 TYR D 25 ARG 0.002 0.000 ARG C 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 122 time to evaluate : 1.406 Fit side-chains REVERT: A 82 LEU cc_start: 0.7388 (tt) cc_final: 0.6706 (mp) REVERT: B 57 ASP cc_start: 0.5651 (t0) cc_final: 0.5169 (p0) REVERT: B 82 LEU cc_start: 0.7384 (tt) cc_final: 0.6698 (mp) REVERT: C 82 LEU cc_start: 0.7372 (tt) cc_final: 0.6708 (mp) REVERT: D 82 LEU cc_start: 0.7373 (tt) cc_final: 0.6709 (mp) REVERT: D 369 MET cc_start: 0.7646 (tpp) cc_final: 0.7434 (tpt) outliers start: 4 outliers final: 0 residues processed: 126 average time/residue: 0.2307 time to fit residues: 43.9822 Evaluate side-chains 115 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13492 Z= 0.221 Angle : 0.618 8.665 18156 Z= 0.289 Chirality : 0.042 0.133 2100 Planarity : 0.004 0.039 2172 Dihedral : 18.226 162.813 2372 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.60 % Allowed : 13.96 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1544 helix: 2.02 (0.18), residues: 928 sheet: -0.42 (0.44), residues: 128 loop : -1.76 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 176 HIS 0.003 0.001 HIS A 149 PHE 0.041 0.002 PHE A 40 TYR 0.013 0.001 TYR D 26 ARG 0.002 0.000 ARG D 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 1.268 Fit side-chains REVERT: A 82 LEU cc_start: 0.7373 (tt) cc_final: 0.6721 (mp) REVERT: B 82 LEU cc_start: 0.7370 (tt) cc_final: 0.6713 (mp) REVERT: C 82 LEU cc_start: 0.7373 (tt) cc_final: 0.6716 (mp) REVERT: D 82 LEU cc_start: 0.7376 (tt) cc_final: 0.6716 (mp) REVERT: D 369 MET cc_start: 0.7786 (tpp) cc_final: 0.7568 (tpt) outliers start: 8 outliers final: 0 residues processed: 130 average time/residue: 0.2300 time to fit residues: 45.1965 Evaluate side-chains 113 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 142 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13492 Z= 0.173 Angle : 0.589 9.019 18156 Z= 0.276 Chirality : 0.041 0.133 2100 Planarity : 0.004 0.038 2172 Dihedral : 17.016 163.380 2372 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.30 % Allowed : 15.97 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.23), residues: 1544 helix: 2.04 (0.18), residues: 928 sheet: -0.53 (0.45), residues: 128 loop : -1.74 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 176 HIS 0.001 0.000 HIS A 149 PHE 0.036 0.001 PHE A 40 TYR 0.008 0.001 TYR C 26 ARG 0.001 0.000 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 132 time to evaluate : 1.457 Fit side-chains REVERT: A 82 LEU cc_start: 0.7359 (tt) cc_final: 0.6761 (mp) REVERT: A 369 MET cc_start: 0.7775 (tpp) cc_final: 0.7523 (tpt) REVERT: B 82 LEU cc_start: 0.7361 (tt) cc_final: 0.6731 (mp) REVERT: B 369 MET cc_start: 0.7775 (tpp) cc_final: 0.7526 (tpt) REVERT: C 82 LEU cc_start: 0.7374 (tt) cc_final: 0.6719 (mp) REVERT: C 369 MET cc_start: 0.7776 (tpp) cc_final: 0.7525 (tpt) REVERT: D 82 LEU cc_start: 0.7377 (tt) cc_final: 0.6722 (mp) outliers start: 4 outliers final: 0 residues processed: 136 average time/residue: 0.2638 time to fit residues: 52.0777 Evaluate side-chains 122 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 1.9990 chunk 85 optimal weight: 0.3980 chunk 2 optimal weight: 0.2980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13492 Z= 0.177 Angle : 0.592 10.109 18156 Z= 0.277 Chirality : 0.041 0.133 2100 Planarity : 0.004 0.036 2172 Dihedral : 16.648 163.468 2372 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.52 % Allowed : 18.73 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.23), residues: 1544 helix: 2.00 (0.18), residues: 928 sheet: -0.59 (0.45), residues: 128 loop : -1.71 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 176 HIS 0.002 0.000 HIS B 149 PHE 0.040 0.001 PHE A 40 TYR 0.006 0.001 TYR C 199 ARG 0.002 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7366 (tt) cc_final: 0.6767 (mp) REVERT: B 82 LEU cc_start: 0.7367 (tt) cc_final: 0.6739 (mp) REVERT: C 82 LEU cc_start: 0.7372 (tt) cc_final: 0.6739 (mp) REVERT: D 82 LEU cc_start: 0.7463 (tt) cc_final: 0.6828 (mp) outliers start: 7 outliers final: 0 residues processed: 128 average time/residue: 0.2694 time to fit residues: 50.2061 Evaluate side-chains 117 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 88 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13492 Z= 0.173 Angle : 0.592 9.139 18156 Z= 0.276 Chirality : 0.042 0.135 2100 Planarity : 0.004 0.035 2172 Dihedral : 16.382 163.689 2372 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.45 % Allowed : 19.78 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.23), residues: 1544 helix: 1.98 (0.18), residues: 924 sheet: -0.57 (0.46), residues: 128 loop : -1.70 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 176 HIS 0.002 0.001 HIS B 149 PHE 0.041 0.001 PHE A 40 TYR 0.008 0.001 TYR D 199 ARG 0.001 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7451 (tt) cc_final: 0.6852 (mp) REVERT: B 82 LEU cc_start: 0.7347 (tt) cc_final: 0.6765 (mp) REVERT: C 82 LEU cc_start: 0.7450 (tt) cc_final: 0.6825 (mp) REVERT: D 82 LEU cc_start: 0.7453 (tt) cc_final: 0.6828 (mp) outliers start: 6 outliers final: 1 residues processed: 139 average time/residue: 0.2610 time to fit residues: 52.9681 Evaluate side-chains 126 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 94 optimal weight: 0.3980 chunk 91 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13492 Z= 0.179 Angle : 0.597 8.807 18156 Z= 0.279 Chirality : 0.042 0.134 2100 Planarity : 0.004 0.035 2172 Dihedral : 16.243 163.530 2372 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.52 % Allowed : 20.75 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.23), residues: 1544 helix: 2.03 (0.18), residues: 924 sheet: -0.53 (0.46), residues: 128 loop : -1.71 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 176 HIS 0.002 0.000 HIS D 149 PHE 0.043 0.001 PHE A 40 TYR 0.008 0.001 TYR D 199 ARG 0.004 0.000 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 138 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7446 (tt) cc_final: 0.6865 (mp) REVERT: B 82 LEU cc_start: 0.7442 (tt) cc_final: 0.6859 (mp) REVERT: C 82 LEU cc_start: 0.7450 (tt) cc_final: 0.6872 (mp) REVERT: D 82 LEU cc_start: 0.7453 (tt) cc_final: 0.6874 (mp) outliers start: 7 outliers final: 0 residues processed: 145 average time/residue: 0.2677 time to fit residues: 56.8716 Evaluate side-chains 131 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN B 412 GLN C 412 GLN D 412 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13492 Z= 0.179 Angle : 0.621 8.854 18156 Z= 0.289 Chirality : 0.042 0.133 2100 Planarity : 0.004 0.035 2172 Dihedral : 16.104 163.811 2372 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.67 % Allowed : 21.34 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.23), residues: 1544 helix: 2.01 (0.18), residues: 924 sheet: -0.45 (0.54), residues: 92 loop : -1.45 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 176 HIS 0.001 0.000 HIS A 149 PHE 0.044 0.001 PHE A 40 TYR 0.008 0.001 TYR D 199 ARG 0.001 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7452 (tt) cc_final: 0.6867 (mp) REVERT: B 82 LEU cc_start: 0.7446 (tt) cc_final: 0.6861 (mp) REVERT: C 82 LEU cc_start: 0.7454 (tt) cc_final: 0.6864 (mp) REVERT: D 82 LEU cc_start: 0.7455 (tt) cc_final: 0.6864 (mp) outliers start: 9 outliers final: 5 residues processed: 154 average time/residue: 0.2639 time to fit residues: 58.9313 Evaluate side-chains 136 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain C residue 412 GLN Chi-restraints excluded: chain D residue 412 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 144 optimal weight: 0.4980 chunk 84 optimal weight: 0.3980 chunk 61 optimal weight: 0.0970 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 126 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN B 412 GLN C 412 GLN D 412 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13492 Z= 0.177 Angle : 0.643 9.012 18156 Z= 0.301 Chirality : 0.042 0.143 2100 Planarity : 0.004 0.035 2172 Dihedral : 16.007 163.965 2372 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.67 % Allowed : 21.79 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.23), residues: 1544 helix: 2.00 (0.18), residues: 924 sheet: -0.35 (0.55), residues: 92 loop : -1.52 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 176 HIS 0.001 0.000 HIS A 149 PHE 0.046 0.002 PHE A 40 TYR 0.010 0.001 TYR A 199 ARG 0.003 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7451 (tt) cc_final: 0.6860 (mp) REVERT: B 82 LEU cc_start: 0.7447 (tt) cc_final: 0.6861 (mp) REVERT: B 234 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7629 (tm-30) REVERT: C 82 LEU cc_start: 0.7442 (tt) cc_final: 0.6824 (mp) REVERT: C 234 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7655 (tm-30) REVERT: D 82 LEU cc_start: 0.7442 (tt) cc_final: 0.6825 (mp) REVERT: D 234 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7651 (tm-30) outliers start: 9 outliers final: 0 residues processed: 141 average time/residue: 0.2695 time to fit residues: 55.1535 Evaluate side-chains 131 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.1485 > 50: distance: 35 - 55: 8.131 distance: 42 - 63: 8.989 distance: 46 - 68: 22.735 distance: 49 - 55: 5.963 distance: 55 - 56: 4.081 distance: 56 - 57: 12.502 distance: 56 - 59: 4.506 distance: 57 - 58: 13.806 distance: 57 - 63: 13.872 distance: 59 - 60: 10.756 distance: 60 - 61: 7.523 distance: 60 - 62: 18.949 distance: 63 - 64: 3.771 distance: 64 - 65: 27.361 distance: 64 - 67: 22.273 distance: 65 - 66: 23.140 distance: 65 - 68: 3.342 distance: 68 - 69: 7.486 distance: 69 - 70: 3.235 distance: 69 - 72: 14.851 distance: 70 - 71: 16.375 distance: 70 - 73: 6.459 distance: 73 - 74: 15.530 distance: 74 - 75: 30.778 distance: 74 - 77: 30.304 distance: 75 - 76: 11.253 distance: 75 - 81: 30.368 distance: 77 - 78: 10.291 distance: 78 - 79: 21.224 distance: 78 - 80: 14.008 distance: 81 - 82: 26.390 distance: 81 - 87: 30.296 distance: 82 - 83: 16.351 distance: 82 - 85: 26.908 distance: 83 - 84: 4.896 distance: 83 - 88: 20.188 distance: 85 - 86: 23.722 distance: 86 - 87: 21.111 distance: 88 - 89: 15.925 distance: 89 - 90: 15.484 distance: 89 - 92: 17.804 distance: 90 - 91: 15.350 distance: 90 - 96: 11.961 distance: 92 - 93: 19.782 distance: 93 - 94: 15.219 distance: 93 - 95: 8.017 distance: 96 - 97: 10.222 distance: 97 - 98: 15.366 distance: 97 - 100: 12.628 distance: 98 - 99: 23.925 distance: 98 - 104: 13.862 distance: 100 - 101: 8.987 distance: 101 - 102: 18.789 distance: 101 - 103: 7.493 distance: 104 - 105: 19.885 distance: 105 - 106: 11.451 distance: 105 - 108: 5.051 distance: 106 - 107: 6.923 distance: 106 - 112: 21.729 distance: 108 - 109: 12.096 distance: 109 - 110: 31.078 distance: 109 - 111: 19.034 distance: 112 - 113: 10.490 distance: 113 - 116: 7.039 distance: 116 - 117: 18.613 distance: 117 - 118: 25.005 distance: 117 - 119: 38.319 distance: 120 - 121: 5.175 distance: 121 - 122: 6.319 distance: 121 - 124: 15.810 distance: 122 - 123: 3.495 distance: 122 - 127: 25.699 distance: 124 - 125: 5.854 distance: 124 - 126: 15.297