Starting phenix.real_space_refine on Fri Dec 8 05:13:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz1_21481/12_2023/6vz1_21481_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz1_21481/12_2023/6vz1_21481.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz1_21481/12_2023/6vz1_21481_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz1_21481/12_2023/6vz1_21481_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz1_21481/12_2023/6vz1_21481_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz1_21481/12_2023/6vz1_21481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz1_21481/12_2023/6vz1_21481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz1_21481/12_2023/6vz1_21481_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz1_21481/12_2023/6vz1_21481_updated.pdb" } resolution = 3.2 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= 0.009 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 10 5.49 5 S 44 5.16 5 C 4736 2.51 5 N 1160 2.21 5 O 1162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 86": "NH1" <-> "NH2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B ARG 318": "NH1" <-> "NH2" Residue "B ARG 362": "NH1" <-> "NH2" Residue "B TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 396": "NH1" <-> "NH2" Residue "B ARG 424": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7112 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3391 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 3391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3391 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 165 Unusual residues: {'3VV': 1, '6OU': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 165 Unusual residues: {'3VV': 1, '6OU': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.25, per 1000 atoms: 0.60 Number of scatterers: 7112 At special positions: 0 Unit cell: (107.07, 94.62, 82.17, 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 44 16.00 P 10 15.00 O 1162 8.00 N 1160 7.00 C 4736 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 - 3.50 Amino acid : False - 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=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.2 seconds 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 0 sheets defined 67.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 88 through 100 Processing helix chain 'A' and resid 103 through 110 removed outlier: 3.833A pdb=" N ILE A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 132 through 156 removed outlier: 4.412A pdb=" N ASN A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 185 removed outlier: 3.606A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Proline residue: A 179 - end of helix removed outlier: 4.286A pdb=" N LEU A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 201 removed outlier: 3.963A pdb=" N LEU A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 227 removed outlier: 3.592A pdb=" N SER A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN A 215 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 249 through 257 Processing helix chain 'A' and resid 275 through 298 removed outlier: 3.750A pdb=" N GLN A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 327 through 341 Processing helix chain 'A' and resid 344 through 352 Processing helix chain 'A' and resid 370 through 375 removed outlier: 4.026A pdb=" N GLN A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 388 removed outlier: 3.665A pdb=" N ARG A 387 " --> pdb=" O LYS A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 395 Processing helix chain 'A' and resid 400 through 418 Processing helix chain 'A' and resid 430 through 447 removed outlier: 3.687A pdb=" N GLN A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE A 438 " --> pdb=" O MET A 434 " (cutoff:3.500A) Proline residue: A 439 - end of helix removed outlier: 3.806A pdb=" N PHE A 443 " --> pdb=" O PRO A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 463 removed outlier: 4.530A pdb=" N ASN A 454 " --> pdb=" O ASN A 451 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 461 " --> pdb=" O TRP A 458 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 463 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 480 removed outlier: 3.638A pdb=" N VAL A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 479 " --> pdb=" O ASP A 475 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 480 " --> pdb=" O TYR A 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 88 through 100 Processing helix chain 'B' and resid 103 through 110 removed outlier: 3.833A pdb=" N ILE B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 132 through 156 removed outlier: 4.412A pdb=" N ASN B 141 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 185 removed outlier: 3.606A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Proline residue: B 179 - end of helix removed outlier: 4.287A pdb=" N LEU B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.964A pdb=" N LEU B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 197 " --> pdb=" O GLY B 193 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 227 removed outlier: 3.592A pdb=" N SER B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN B 215 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 249 through 257 Processing helix chain 'B' and resid 275 through 298 removed outlier: 3.750A pdb=" N GLN B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 318 through 323 Processing helix chain 'B' and resid 327 through 341 Processing helix chain 'B' and resid 344 through 352 Processing helix chain 'B' and resid 370 through 375 removed outlier: 4.026A pdb=" N GLN B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 388 removed outlier: 3.665A pdb=" N ARG B 387 " --> pdb=" O LYS B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 395 Processing helix chain 'B' and resid 400 through 418 Processing helix chain 'B' and resid 430 through 447 removed outlier: 3.687A pdb=" N GLN B 437 " --> pdb=" O GLY B 433 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE B 438 " --> pdb=" O MET B 434 " (cutoff:3.500A) Proline residue: B 439 - end of helix removed outlier: 3.805A pdb=" N PHE B 443 " --> pdb=" O PRO B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 463 removed outlier: 4.530A pdb=" N ASN B 454 " --> pdb=" O ASN B 451 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 461 " --> pdb=" O TRP B 458 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE B 463 " --> pdb=" O SER B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 480 removed outlier: 3.638A pdb=" N VAL B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR B 472 " --> pdb=" O ALA B 468 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 479 " --> pdb=" O ASP B 475 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN B 480 " --> pdb=" O TYR B 476 " (cutoff:3.500A) 318 hydrogen bonds defined for protein. 906 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: 1.93 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1000 1.31 - 1.43: 2216 1.43 - 1.56: 4022 1.56 - 1.69: 18 1.69 - 1.81: 72 Bond restraints: 7328 Sorted by residual: bond pdb=" C49 3VV B 503 " pdb=" C50 3VV B 503 " ideal model delta sigma weight residual 1.291 1.561 -0.270 2.00e-02 2.50e+03 1.83e+02 bond pdb=" C49 3VV A 503 " pdb=" C50 3VV A 503 " ideal model delta sigma weight residual 1.291 1.541 -0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" C49 3VV B 503 " pdb=" O48 3VV B 503 " ideal model delta sigma weight residual 1.621 1.414 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C49 3VV A 503 " pdb=" O48 3VV A 503 " ideal model delta sigma weight residual 1.621 1.416 0.205 2.00e-02 2.50e+03 1.06e+02 bond pdb=" O37 3VV B 503 " pdb=" P38 3VV B 503 " ideal model delta sigma weight residual 1.662 1.504 0.158 2.00e-02 2.50e+03 6.23e+01 ... (remaining 7323 not shown) Histogram of bond angle deviations from ideal: 84.85 - 94.71: 1 94.71 - 104.56: 135 104.56 - 114.42: 4365 114.42 - 124.28: 5191 124.28 - 134.13: 236 Bond angle restraints: 9928 Sorted by residual: angle pdb=" C09 3VV A 503 " pdb=" C10 3VV A 503 " pdb=" C11 3VV A 503 " ideal model delta sigma weight residual 152.65 125.61 27.04 3.00e+00 1.11e-01 8.12e+01 angle pdb=" C09 3VV B 503 " pdb=" C10 3VV B 503 " pdb=" C11 3VV B 503 " ideal model delta sigma weight residual 152.65 127.97 24.68 3.00e+00 1.11e-01 6.77e+01 angle pdb=" O37 3VV B 503 " pdb=" P38 3VV B 503 " pdb=" O41 3VV B 503 " ideal model delta sigma weight residual 109.45 84.85 24.60 3.00e+00 1.11e-01 6.72e+01 angle pdb=" C21 6OU A 501 " pdb=" O22 6OU A 501 " pdb=" P23 6OU A 501 " ideal model delta sigma weight residual 117.17 133.97 -16.80 3.00e+00 1.11e-01 3.14e+01 angle pdb=" C21 6OU B 501 " pdb=" O22 6OU B 501 " pdb=" P23 6OU B 501 " ideal model delta sigma weight residual 117.17 133.71 -16.54 3.00e+00 1.11e-01 3.04e+01 ... (remaining 9923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 4154 35.31 - 70.61: 113 70.61 - 105.92: 20 105.92 - 141.22: 15 141.22 - 176.53: 4 Dihedral angle restraints: 4306 sinusoidal: 1864 harmonic: 2442 Sorted by residual: dihedral pdb=" CA GLY A 87 " pdb=" C GLY A 87 " pdb=" N ILE A 88 " pdb=" CA ILE A 88 " ideal model delta harmonic sigma weight residual 180.00 153.17 26.83 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA GLY B 87 " pdb=" C GLY B 87 " pdb=" N ILE B 88 " pdb=" CA ILE B 88 " ideal model delta harmonic sigma weight residual 180.00 153.22 26.78 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" C34 6OU A 502 " pdb=" C31 6OU A 502 " pdb=" C33 6OU A 502 " pdb=" O30 6OU A 502 " ideal model delta sinusoidal sigma weight residual 180.29 3.76 176.53 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 4303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 1029 0.123 - 0.247: 17 0.247 - 0.370: 4 0.370 - 0.494: 1 0.494 - 0.617: 1 Chirality restraints: 1052 Sorted by residual: chirality pdb=" C31 3VV B 503 " pdb=" C29 3VV B 503 " pdb=" C33 3VV B 503 " pdb=" O32 3VV B 503 " both_signs ideal model delta sigma weight residual False -2.53 -1.92 -0.62 2.00e-01 2.50e+01 9.53e+00 chirality pdb=" C31 3VV A 503 " pdb=" C29 3VV A 503 " pdb=" C33 3VV A 503 " pdb=" O32 3VV A 503 " both_signs ideal model delta sigma weight residual False -2.53 -2.14 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" C50 3VV A 503 " pdb=" C49 3VV A 503 " pdb=" C52 3VV A 503 " pdb=" O51 3VV A 503 " both_signs ideal model delta sigma weight residual False -2.38 -2.69 0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 1049 not shown) Planarity restraints: 1196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C49 3VV B 503 " -0.227 2.00e-02 2.50e+03 9.67e-02 2.57e+02 pdb=" C59 3VV B 503 " 0.076 2.00e-02 2.50e+03 pdb=" C61 3VV B 503 " 0.046 2.00e-02 2.50e+03 pdb=" C62 3VV B 503 " -0.039 2.00e-02 2.50e+03 pdb=" C65 3VV B 503 " 0.045 2.00e-02 2.50e+03 pdb=" C67 3VV B 503 " 0.067 2.00e-02 2.50e+03 pdb=" N58 3VV B 503 " 0.029 2.00e-02 2.50e+03 pdb=" N60 3VV B 503 " 0.080 2.00e-02 2.50e+03 pdb=" N63 3VV B 503 " -0.131 2.00e-02 2.50e+03 pdb=" N64 3VV B 503 " -0.043 2.00e-02 2.50e+03 pdb=" N66 3VV B 503 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 3VV B 503 " 0.061 2.00e-02 2.50e+03 4.98e-02 3.10e+01 pdb=" C24 3VV B 503 " -0.034 2.00e-02 2.50e+03 pdb=" C26 3VV B 503 " 0.052 2.00e-02 2.50e+03 pdb=" N23 3VV B 503 " -0.069 2.00e-02 2.50e+03 pdb=" O25 3VV B 503 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 3VV A 503 " -0.048 2.00e-02 2.50e+03 3.93e-02 1.93e+01 pdb=" C29 3VV A 503 " 0.016 2.00e-02 2.50e+03 pdb=" C31 3VV A 503 " -0.037 2.00e-02 2.50e+03 pdb=" N28 3VV A 503 " 0.061 2.00e-02 2.50e+03 pdb=" O30 3VV A 503 " 0.008 2.00e-02 2.50e+03 ... (remaining 1193 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 37 2.47 - 3.08: 5094 3.08 - 3.69: 10536 3.69 - 4.29: 15820 4.29 - 4.90: 26139 Nonbonded interactions: 57626 Sorted by model distance: nonbonded pdb=" OH TYR B 390 " pdb=" O43 3VV B 503 " model vdw 1.864 2.440 nonbonded pdb=" O GLU B 416 " pdb=" OG SER B 420 " model vdw 2.065 2.440 nonbonded pdb=" O GLU A 416 " pdb=" OG SER A 420 " model vdw 2.065 2.440 nonbonded pdb=" O39 3VV B 503 " pdb=" O45 3VV B 503 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR A 390 " pdb=" O43 3VV A 503 " model vdw 2.216 2.440 ... (remaining 57621 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.410 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: 0.000 Extract box with map and model: 3.920 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.100 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:3.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.014 0.270 7328 Z= 0.886 Angle : 1.252 27.037 9928 Z= 0.532 Chirality : 0.059 0.617 1052 Planarity : 0.006 0.097 1196 Dihedral : 20.456 176.527 2722 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.04 % Favored : 87.96 % Rotamer: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % 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: -4.38 (0.25), residues: 814 helix: -2.37 (0.18), residues: 590 sheet: None (None), residues: 0 loop : -3.92 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 377 HIS 0.012 0.002 HIS B 168 PHE 0.021 0.002 PHE A 277 TYR 0.019 0.002 TYR B 417 ARG 0.003 0.000 ARG B 396 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.751 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2163 time to fit residues: 37.4385 Evaluate side-chains 98 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.792 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 0.0170 chunk 47 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 246 ASN ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 246 ASN ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7328 Z= 0.181 Angle : 0.597 8.210 9928 Z= 0.287 Chirality : 0.041 0.292 1052 Planarity : 0.004 0.034 1196 Dihedral : 20.823 178.420 1166 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.81 % Allowed : 12.26 % Favored : 85.93 % 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: -2.46 (0.28), residues: 814 helix: -0.94 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -3.31 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 340 HIS 0.002 0.001 HIS A 415 PHE 0.013 0.001 PHE B 443 TYR 0.009 0.001 TYR A 339 ARG 0.006 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 0.778 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 138 average time/residue: 0.1762 time to fit residues: 33.5657 Evaluate side-chains 121 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 0.821 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0741 time to fit residues: 2.2013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7328 Z= 0.250 Angle : 0.603 9.241 9928 Z= 0.291 Chirality : 0.041 0.164 1052 Planarity : 0.004 0.033 1196 Dihedral : 20.136 179.292 1166 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 1.25 % Allowed : 15.46 % Favored : 83.29 % 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: -1.92 (0.29), residues: 814 helix: -0.48 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -3.23 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 340 HIS 0.003 0.001 HIS B 415 PHE 0.016 0.002 PHE A 443 TYR 0.012 0.001 TYR A 339 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 0.869 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 125 average time/residue: 0.1916 time to fit residues: 32.4398 Evaluate side-chains 117 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 0.793 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0738 time to fit residues: 1.7807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 50 optimal weight: 0.4980 chunk 74 optimal weight: 6.9990 chunk 79 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7328 Z= 0.227 Angle : 0.582 9.817 9928 Z= 0.280 Chirality : 0.040 0.122 1052 Planarity : 0.004 0.032 1196 Dihedral : 19.765 179.774 1166 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 1.11 % Allowed : 16.99 % Favored : 81.89 % 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: -1.60 (0.29), residues: 814 helix: -0.21 (0.22), residues: 584 sheet: None (None), residues: 0 loop : -3.19 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 340 HIS 0.005 0.001 HIS B 415 PHE 0.015 0.001 PHE A 443 TYR 0.011 0.001 TYR A 339 ARG 0.002 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 0.831 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 121 average time/residue: 0.1728 time to fit residues: 29.0907 Evaluate side-chains 117 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 0.712 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0786 time to fit residues: 1.8315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7328 Z= 0.172 Angle : 0.557 9.832 9928 Z= 0.267 Chirality : 0.039 0.115 1052 Planarity : 0.004 0.030 1196 Dihedral : 19.064 177.290 1166 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.56 % Allowed : 18.25 % Favored : 81.20 % 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: -1.20 (0.30), residues: 814 helix: 0.13 (0.22), residues: 582 sheet: None (None), residues: 0 loop : -3.14 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 340 HIS 0.003 0.000 HIS B 415 PHE 0.016 0.001 PHE A 443 TYR 0.010 0.001 TYR A 339 ARG 0.002 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 0.817 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 119 average time/residue: 0.1881 time to fit residues: 30.6780 Evaluate side-chains 118 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 0.817 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0714 time to fit residues: 1.5322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7328 Z= 0.186 Angle : 0.559 10.418 9928 Z= 0.265 Chirality : 0.039 0.112 1052 Planarity : 0.004 0.029 1196 Dihedral : 18.331 172.791 1166 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.28 % Allowed : 19.08 % Favored : 80.64 % 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: -0.95 (0.30), residues: 814 helix: 0.32 (0.22), residues: 582 sheet: None (None), residues: 0 loop : -3.07 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 131 HIS 0.003 0.001 HIS B 415 PHE 0.016 0.001 PHE A 443 TYR 0.010 0.001 TYR A 339 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 0.807 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 116 average time/residue: 0.1857 time to fit residues: 29.6204 Evaluate side-chains 114 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 0.741 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0728 time to fit residues: 1.4059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 0.3980 chunk 79 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7328 Z= 0.157 Angle : 0.544 10.406 9928 Z= 0.257 Chirality : 0.038 0.114 1052 Planarity : 0.004 0.028 1196 Dihedral : 17.622 167.048 1166 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.28 % Allowed : 20.06 % Favored : 79.67 % 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: -0.73 (0.30), residues: 814 helix: 0.52 (0.23), residues: 580 sheet: None (None), residues: 0 loop : -3.07 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 340 HIS 0.002 0.000 HIS B 415 PHE 0.016 0.001 PHE A 443 TYR 0.009 0.001 TYR A 339 ARG 0.002 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 0.793 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 121 average time/residue: 0.1828 time to fit residues: 30.4838 Evaluate side-chains 113 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 0.804 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1084 time to fit residues: 1.2526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.3980 chunk 15 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7328 Z= 0.185 Angle : 0.566 10.929 9928 Z= 0.265 Chirality : 0.038 0.115 1052 Planarity : 0.004 0.027 1196 Dihedral : 17.385 165.916 1166 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.11 % Allowed : 19.92 % Favored : 78.97 % 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: -0.67 (0.31), residues: 814 helix: 0.59 (0.23), residues: 578 sheet: None (None), residues: 0 loop : -3.08 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 340 HIS 0.002 0.001 HIS B 415 PHE 0.016 0.001 PHE A 443 TYR 0.010 0.001 TYR A 339 ARG 0.002 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 0.877 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 116 average time/residue: 0.1928 time to fit residues: 31.1227 Evaluate side-chains 116 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 0.801 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0797 time to fit residues: 1.9995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7328 Z= 0.165 Angle : 0.557 10.601 9928 Z= 0.260 Chirality : 0.038 0.111 1052 Planarity : 0.004 0.027 1196 Dihedral : 16.881 164.799 1166 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.28 % Allowed : 19.92 % Favored : 79.81 % 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: -0.51 (0.31), residues: 814 helix: 0.70 (0.23), residues: 578 sheet: None (None), residues: 0 loop : -3.02 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 377 HIS 0.002 0.000 HIS B 168 PHE 0.015 0.001 PHE A 443 TYR 0.010 0.001 TYR B 339 ARG 0.001 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 0.803 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 111 average time/residue: 0.1844 time to fit residues: 28.1569 Evaluate side-chains 107 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 0.748 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0989 time to fit residues: 1.1579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 0.0470 chunk 50 optimal weight: 8.9990 chunk 39 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7328 Z= 0.147 Angle : 0.545 10.353 9928 Z= 0.253 Chirality : 0.037 0.110 1052 Planarity : 0.003 0.027 1196 Dihedral : 16.192 164.691 1166 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.42 % Allowed : 20.75 % Favored : 78.83 % 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: -0.36 (0.31), residues: 814 helix: 0.82 (0.23), residues: 578 sheet: None (None), residues: 0 loop : -2.99 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 377 HIS 0.001 0.000 HIS B 168 PHE 0.015 0.001 PHE A 443 TYR 0.011 0.001 TYR B 339 ARG 0.002 0.000 ARG A 395 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 0.788 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 116 average time/residue: 0.1750 time to fit residues: 28.3590 Evaluate side-chains 108 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0701 time to fit residues: 1.3511 ------------------------------------------------------------------------------- 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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 56.8242 > 50: distance: 1 - 23: 15.649 distance: 8 - 34: 20.232 distance: 15 - 42: 17.234 distance: 19 - 23: 15.755 distance: 23 - 24: 14.246 distance: 24 - 25: 23.716 distance: 24 - 27: 3.650 distance: 25 - 26: 23.815 distance: 25 - 34: 23.186 distance: 27 - 28: 14.170 distance: 28 - 29: 15.230 distance: 29 - 30: 16.156 distance: 30 - 31: 10.219 distance: 31 - 32: 12.388 distance: 31 - 33: 10.438 distance: 34 - 35: 15.440 distance: 35 - 36: 9.568 distance: 35 - 38: 13.241 distance: 36 - 37: 20.155 distance: 36 - 42: 12.143 distance: 38 - 39: 18.230 distance: 39 - 40: 19.895 distance: 39 - 41: 23.007 distance: 42 - 43: 13.023 distance: 43 - 44: 17.144 distance: 43 - 46: 15.314 distance: 44 - 45: 12.273 distance: 44 - 47: 17.278 distance: 47 - 48: 23.812 distance: 48 - 49: 16.435 distance: 48 - 51: 19.687 distance: 49 - 50: 9.559 distance: 49 - 54: 27.232 distance: 51 - 52: 10.201 distance: 51 - 53: 29.165 distance: 54 - 55: 29.039 distance: 55 - 56: 22.668 distance: 56 - 57: 17.439 distance: 56 - 58: 12.527 distance: 58 - 59: 31.750 distance: 59 - 60: 14.620 distance: 59 - 62: 25.299 distance: 60 - 61: 19.985 distance: 60 - 63: 6.815 distance: 63 - 64: 20.158 distance: 64 - 65: 8.515 distance: 64 - 67: 24.247 distance: 65 - 66: 21.767 distance: 65 - 71: 6.109 distance: 67 - 68: 15.520 distance: 68 - 69: 32.911 distance: 68 - 70: 40.200 distance: 71 - 72: 25.839 distance: 72 - 73: 12.385 distance: 72 - 75: 18.109 distance: 73 - 74: 9.446 distance: 73 - 78: 3.816 distance: 75 - 76: 16.454 distance: 75 - 77: 13.788 distance: 78 - 79: 10.727 distance: 79 - 80: 3.085 distance: 79 - 82: 15.018 distance: 80 - 81: 3.501 distance: 80 - 87: 14.059 distance: 81 - 104: 30.426 distance: 82 - 83: 24.228 distance: 83 - 84: 13.380 distance: 84 - 85: 20.528 distance: 84 - 86: 18.734 distance: 88 - 89: 19.116 distance: 88 - 91: 15.601 distance: 89 - 90: 5.626 distance: 89 - 96: 7.213 distance: 90 - 111: 14.489 distance: 91 - 92: 17.914 distance: 92 - 93: 14.688 distance: 93 - 94: 20.103 distance: 93 - 95: 19.794