Starting phenix.real_space_refine on Mon Mar 11 14:23:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yud_34104/03_2024/7yud_34104_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yud_34104/03_2024/7yud_34104.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yud_34104/03_2024/7yud_34104_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yud_34104/03_2024/7yud_34104_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yud_34104/03_2024/7yud_34104_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yud_34104/03_2024/7yud_34104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yud_34104/03_2024/7yud_34104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yud_34104/03_2024/7yud_34104_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yud_34104/03_2024/7yud_34104_neut_updated.pdb" } resolution = 2.98 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= -0.002 sd= 0.132 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 1 5.49 5 S 41 5.16 5 C 5391 2.51 5 N 1410 2.21 5 O 1598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 88": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8441 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1732 Classifications: {'peptide': 229} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 217} Chain: "L" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1619 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain: "N" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 959 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "R" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3183 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 12, 'TRANS': 404} Chain breaks: 2 Chain: "K" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'J89': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.97, per 1000 atoms: 0.59 Number of scatterers: 8441 At special positions: 0 Unit cell: (82.5, 88, 162.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 P 1 15.00 O 1598 8.00 N 1410 7.00 C 5391 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 26 " - pdb=" SG CYS H 100 " distance=2.05 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 215 " distance=2.04 Simple disulfide: pdb=" SG CYS L 25 " - pdb=" SG CYS L 90 " distance=2.05 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 97 " distance=2.05 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 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=0, symmetry=0 Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.7 seconds 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 14 sheets defined 34.8% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'H' and resid 33 through 35 No H-bonds generated for 'chain 'H' and resid 33 through 35' Processing helix chain 'H' and resid 92 through 94 No H-bonds generated for 'chain 'H' and resid 92 through 94' Processing helix chain 'H' and resid 147 through 149 No H-bonds generated for 'chain 'H' and resid 147 through 149' Processing helix chain 'H' and resid 174 through 176 No H-bonds generated for 'chain 'H' and resid 174 through 176' Processing helix chain 'H' and resid 206 through 209 Processing helix chain 'L' and resid 124 through 129 Processing helix chain 'L' and resid 185 through 190 removed outlier: 3.720A pdb=" N LYS L 190 " --> pdb=" O ALA L 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 91 No H-bonds generated for 'chain 'N' and resid 89 through 91' Processing helix chain 'R' and resid 101 through 117 Processing helix chain 'R' and resid 123 through 132 removed outlier: 5.651A pdb=" N LEU R 127 " --> pdb=" O GLY R 124 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN R 130 " --> pdb=" O LEU R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 164 removed outlier: 3.985A pdb=" N LEU R 142 " --> pdb=" O ARG R 138 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU R 143 " --> pdb=" O GLY R 139 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLN R 144 " --> pdb=" O ALA R 140 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE R 147 " --> pdb=" O LEU R 143 " (cutoff:3.500A) Proline residue: R 156 - end of helix removed outlier: 3.775A pdb=" N ASP R 163 " --> pdb=" O GLY R 159 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG R 164 " --> pdb=" O TYR R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 187 removed outlier: 4.125A pdb=" N SER R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N PHE R 187 " --> pdb=" O PHE R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 194 through 221 removed outlier: 3.907A pdb=" N TYR R 210 " --> pdb=" O GLY R 206 " (cutoff:3.500A) Proline residue: R 215 - end of helix removed outlier: 3.582A pdb=" N LEU R 221 " --> pdb=" O ILE R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 256 removed outlier: 4.353A pdb=" N ALA R 237 " --> pdb=" O VAL R 233 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ILE R 238 " --> pdb=" O PHE R 234 " (cutoff:3.500A) Proline residue: R 239 - end of helix removed outlier: 3.775A pdb=" N TYR R 246 " --> pdb=" O SER R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 263 Processing helix chain 'R' and resid 265 through 278 removed outlier: 4.159A pdb=" N LEU R 269 " --> pdb=" O VAL R 265 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU R 278 " --> pdb=" O GLY R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 303 through 309 removed outlier: 4.090A pdb=" N ALA R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 346 Proline residue: R 337 - end of helix Processing helix chain 'R' and resid 362 through 390 removed outlier: 3.912A pdb=" N PHE R 372 " --> pdb=" O ALA R 368 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE R 375 " --> pdb=" O CYS R 371 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL R 378 " --> pdb=" O GLY R 374 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU R 390 " --> pdb=" O ARG R 386 " (cutoff:3.500A) Processing helix chain 'R' and resid 395 through 419 removed outlier: 4.062A pdb=" N LEU R 413 " --> pdb=" O ILE R 409 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE R 414 " --> pdb=" O PHE R 410 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE R 415 " --> pdb=" O ILE R 411 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL R 416 " --> pdb=" O CYS R 412 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LYS R 419 " --> pdb=" O PHE R 415 " (cutoff:3.500A) Processing helix chain 'R' and resid 423 through 437 removed outlier: 3.747A pdb=" N PHE R 437 " --> pdb=" O GLU R 433 " (cutoff:3.500A) Processing helix chain 'R' and resid 443 through 450 Processing helix chain 'R' and resid 453 through 470 removed outlier: 3.988A pdb=" N ARG R 456 " --> pdb=" O PRO R 453 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA R 457 " --> pdb=" O THR R 454 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL R 460 " --> pdb=" O ALA R 457 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU R 470 " --> pdb=" O SER R 467 " (cutoff:3.500A) Processing helix chain 'R' and resid 475 through 489 removed outlier: 4.169A pdb=" N SER R 489 " --> pdb=" O LEU R 485 " (cutoff:3.500A) Processing helix chain 'R' and resid 494 through 540 removed outlier: 3.902A pdb=" N LEU R 501 " --> pdb=" O GLU R 497 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET R 506 " --> pdb=" O GLY R 502 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU R 507 " --> pdb=" O TYR R 503 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N CYS R 508 " --> pdb=" O ALA R 504 " (cutoff:3.500A) Proline residue: R 509 - end of helix removed outlier: 4.083A pdb=" N PHE R 525 " --> pdb=" O ALA R 521 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N VAL R 527 " --> pdb=" O ALA R 523 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N SER R 528 " --> pdb=" O LEU R 524 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'H' and resid 7 through 11 Processing sheet with id= B, first strand: chain 'H' and resid 14 through 16 removed outlier: 6.173A pdb=" N ARG H 42 " --> pdb=" O TRP H 51 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TRP H 51 " --> pdb=" O ARG H 42 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ALA H 44 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU H 49 " --> pdb=" O ALA H 44 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 139 through 143 removed outlier: 6.066A pdb=" N TYR H 195 " --> pdb=" O ASP H 163 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 170 through 173 removed outlier: 4.327A pdb=" N TYR H 213 " --> pdb=" O VAL H 230 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 7 through 9 Processing sheet with id= F, first strand: chain 'L' and resid 12 through 15 removed outlier: 6.257A pdb=" N LYS L 105 " --> pdb=" O LEU L 13 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ALA L 15 " --> pdb=" O LYS L 105 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLU L 107 " --> pdb=" O ALA L 15 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'L' and resid 98 through 100 removed outlier: 6.300A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.953A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 146 through 152 Processing sheet with id= J, first strand: chain 'N' and resid 5 through 7 Processing sheet with id= K, first strand: chain 'N' and resid 10 through 12 removed outlier: 4.613A pdb=" N LEU N 35 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE N 52 " --> pdb=" O LEU N 35 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ARG N 39 " --> pdb=" O GLY N 48 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLY N 48 " --> pdb=" O ARG N 39 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 98 through 100 Processing sheet with id= M, first strand: chain 'K' and resid 3 through 7 Processing sheet with id= N, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.773A pdb=" N SER K 120 " --> pdb=" O VAL K 12 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA K 33 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1149 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: 2.61 Time building geometry restraints manager: 3.41 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: 2652 1.34 - 1.47: 2343 1.47 - 1.60: 3581 1.60 - 1.73: 1 1.73 - 1.85: 60 Bond restraints: 8637 Sorted by residual: bond pdb=" O21 J89 R 601 " pdb=" P22 J89 R 601 " ideal model delta sigma weight residual 1.648 1.853 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C17 J89 R 601 " pdb=" C20 J89 R 601 " ideal model delta sigma weight residual 1.527 1.672 -0.145 2.00e-02 2.50e+03 5.25e+01 bond pdb=" N TYR H 104 " pdb=" CA TYR H 104 " ideal model delta sigma weight residual 1.458 1.490 -0.031 9.00e-03 1.23e+04 1.22e+01 bond pdb=" C20 J89 R 601 " pdb=" O21 J89 R 601 " ideal model delta sigma weight residual 1.399 1.333 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" N ASN H 116 " pdb=" CA ASN H 116 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.18e+00 ... (remaining 8632 not shown) Histogram of bond angle deviations from ideal: 98.32 - 105.50: 164 105.50 - 112.68: 4445 112.68 - 119.86: 2980 119.86 - 127.05: 4048 127.05 - 134.23: 96 Bond angle restraints: 11733 Sorted by residual: angle pdb=" N GLY H 117 " pdb=" CA GLY H 117 " pdb=" C GLY H 117 " ideal model delta sigma weight residual 112.50 119.67 -7.17 1.16e+00 7.43e-01 3.82e+01 angle pdb=" N THR N 34 " pdb=" CA THR N 34 " pdb=" C THR N 34 " ideal model delta sigma weight residual 114.75 121.94 -7.19 1.26e+00 6.30e-01 3.25e+01 angle pdb=" N LEU N 35 " pdb=" CA LEU N 35 " pdb=" C LEU N 35 " ideal model delta sigma weight residual 109.06 117.45 -8.39 1.70e+00 3.46e-01 2.44e+01 angle pdb=" N TYR N 33 " pdb=" CA TYR N 33 " pdb=" C TYR N 33 " ideal model delta sigma weight residual 109.23 101.61 7.62 1.55e+00 4.16e-01 2.42e+01 angle pdb=" N ARG R 164 " pdb=" CA ARG R 164 " pdb=" C ARG R 164 " ideal model delta sigma weight residual 111.40 117.20 -5.80 1.22e+00 6.72e-01 2.26e+01 ... (remaining 11728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.56: 4780 21.56 - 43.11: 237 43.11 - 64.67: 18 64.67 - 86.22: 16 86.22 - 107.78: 2 Dihedral angle restraints: 5053 sinusoidal: 1890 harmonic: 3163 Sorted by residual: dihedral pdb=" CB CYS H 159 " pdb=" SG CYS H 159 " pdb=" SG CYS H 215 " pdb=" CB CYS H 215 " ideal model delta sinusoidal sigma weight residual 93.00 56.21 36.79 1 1.00e+01 1.00e-02 1.91e+01 dihedral pdb=" C THR N 34 " pdb=" N THR N 34 " pdb=" CA THR N 34 " pdb=" CB THR N 34 " ideal model delta harmonic sigma weight residual -122.00 -132.22 10.22 0 2.50e+00 1.60e-01 1.67e+01 dihedral pdb=" CA HIS H 110 " pdb=" C HIS H 110 " pdb=" N ALA H 111 " pdb=" CA ALA H 111 " ideal model delta harmonic sigma weight residual 180.00 160.16 19.84 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 5050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1295 0.128 - 0.255: 19 0.255 - 0.383: 2 0.383 - 0.511: 1 0.511 - 0.638: 1 Chirality restraints: 1318 Sorted by residual: chirality pdb=" CG LEU N 35 " pdb=" CB LEU N 35 " pdb=" CD1 LEU N 35 " pdb=" CD2 LEU N 35 " both_signs ideal model delta sigma weight residual False -2.59 -1.95 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA THR N 34 " pdb=" N THR N 34 " pdb=" C THR N 34 " pdb=" CB THR N 34 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" CA HIS H 110 " pdb=" N HIS H 110 " pdb=" C HIS H 110 " pdb=" CB HIS H 110 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 1315 not shown) Planarity restraints: 1477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 178 " 0.043 2.00e-02 2.50e+03 2.18e-02 1.18e+01 pdb=" CG TRP R 178 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP R 178 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP R 178 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP R 178 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP R 178 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP R 178 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 178 " 0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 178 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 178 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR N 122 " -0.054 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO N 123 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO N 123 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO N 123 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 110 " 0.032 2.00e-02 2.50e+03 2.67e-02 1.07e+01 pdb=" CG HIS H 110 " -0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS H 110 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 HIS H 110 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 HIS H 110 " 0.023 2.00e-02 2.50e+03 pdb=" NE2 HIS H 110 " 0.023 2.00e-02 2.50e+03 ... (remaining 1474 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2553 2.82 - 3.34: 7046 3.34 - 3.86: 12856 3.86 - 4.38: 14320 4.38 - 4.90: 26800 Nonbonded interactions: 63575 Sorted by model distance: nonbonded pdb=" OG SER K 35 " pdb=" OH TYR K 108 " model vdw 2.303 2.440 nonbonded pdb=" OG1 THR N 34 " pdb=" NH2 ARG N 73 " model vdw 2.308 2.520 nonbonded pdb=" OG SER R 250 " pdb=" OG SER R 363 " model vdw 2.313 2.440 nonbonded pdb=" O CYS N 104 " pdb=" ND2 ASN R 538 " model vdw 2.360 2.520 nonbonded pdb=" O TRP H 115 " pdb=" OG SER L 52 " model vdw 2.402 2.440 ... (remaining 63570 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 4.080 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 26.680 Find NCS groups from input model: 0.250 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: 0.000 Load rotamer database and sin/cos tables:13.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.205 8637 Z= 0.525 Angle : 0.954 11.389 11733 Z= 0.528 Chirality : 0.057 0.638 1318 Planarity : 0.006 0.083 1477 Dihedral : 13.244 107.776 3025 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.42 (0.25), residues: 1091 helix: 0.66 (0.27), residues: 367 sheet: 0.33 (0.29), residues: 316 loop : -1.62 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP R 178 HIS 0.017 0.002 HIS H 110 PHE 0.056 0.003 PHE R 526 TYR 0.030 0.002 TYR N 33 ARG 0.007 0.001 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.981 Fit side-chains REVERT: H 77 ASP cc_start: 0.7586 (t70) cc_final: 0.7201 (t0) REVERT: R 258 ASP cc_start: 0.7548 (t0) cc_final: 0.7291 (t70) REVERT: R 500 SER cc_start: 0.8209 (m) cc_final: 0.7986 (m) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 1.2253 time to fit residues: 126.7406 Evaluate side-chains 80 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.0040 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 ASN H 116 ASN R 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8637 Z= 0.180 Angle : 0.593 7.715 11733 Z= 0.319 Chirality : 0.044 0.224 1318 Planarity : 0.005 0.058 1477 Dihedral : 6.852 97.929 1218 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.88 % Allowed : 6.71 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.21 (0.26), residues: 1091 helix: 1.27 (0.29), residues: 366 sheet: 0.69 (0.30), residues: 314 loop : -1.34 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 178 HIS 0.006 0.001 HIS H 110 PHE 0.019 0.001 PHE R 526 TYR 0.018 0.001 TYR R 160 ARG 0.007 0.000 ARG R 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 1.017 Fit side-chains REVERT: N 28 ARG cc_start: 0.7525 (mmt90) cc_final: 0.7171 (mmt-90) REVERT: N 108 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7453 (ttp) REVERT: R 500 SER cc_start: 0.8186 (m) cc_final: 0.7971 (m) outliers start: 8 outliers final: 3 residues processed: 86 average time/residue: 1.3514 time to fit residues: 123.6650 Evaluate side-chains 80 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 108 MET Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 0.0040 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 ASN N 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8637 Z= 0.157 Angle : 0.535 6.810 11733 Z= 0.288 Chirality : 0.042 0.192 1318 Planarity : 0.005 0.058 1477 Dihedral : 6.334 86.918 1218 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.43 % Allowed : 8.47 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.55 (0.26), residues: 1091 helix: 1.51 (0.29), residues: 366 sheet: 0.84 (0.30), residues: 314 loop : -1.08 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 178 HIS 0.006 0.001 HIS H 110 PHE 0.015 0.001 PHE R 526 TYR 0.019 0.001 TYR R 160 ARG 0.005 0.000 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 1.047 Fit side-chains REVERT: L 6 MET cc_start: 0.8284 (mtm) cc_final: 0.7716 (mtm) REVERT: N 28 ARG cc_start: 0.7481 (mmt90) cc_final: 0.7168 (mmt-90) REVERT: N 58 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7604 (mt) REVERT: N 108 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7311 (ttp) REVERT: R 254 GLN cc_start: 0.7824 (tp40) cc_final: 0.7379 (tm-30) REVERT: R 500 SER cc_start: 0.8179 (m) cc_final: 0.7961 (m) REVERT: R 534 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7219 (mt-10) outliers start: 13 outliers final: 6 residues processed: 94 average time/residue: 1.2334 time to fit residues: 123.7746 Evaluate side-chains 87 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 216 ASN Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 108 MET Chi-restraints excluded: chain R residue 307 LYS Chi-restraints excluded: chain R residue 409 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 0.0270 chunk 28 optimal weight: 6.9990 overall best weight: 1.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 190 GLN L 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8637 Z= 0.332 Angle : 0.655 7.779 11733 Z= 0.355 Chirality : 0.047 0.317 1318 Planarity : 0.005 0.066 1477 Dihedral : 6.410 78.091 1218 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.53 % Allowed : 10.34 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.31 (0.26), residues: 1091 helix: 1.17 (0.28), residues: 368 sheet: 1.08 (0.32), residues: 284 loop : -1.23 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 178 HIS 0.010 0.001 HIS H 110 PHE 0.022 0.002 PHE R 526 TYR 0.026 0.002 TYR N 33 ARG 0.004 0.000 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 82 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: H 47 LYS cc_start: 0.8291 (mtmt) cc_final: 0.7993 (mtpt) REVERT: H 54 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.7884 (t80) REVERT: L 6 MET cc_start: 0.8398 (mtm) cc_final: 0.7799 (mtm) REVERT: N 28 ARG cc_start: 0.7485 (mmt90) cc_final: 0.7119 (mmt-90) REVERT: N 58 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7771 (mt) REVERT: N 108 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7288 (ttp) REVERT: R 254 GLN cc_start: 0.7811 (tp40) cc_final: 0.7444 (tm-30) REVERT: R 500 SER cc_start: 0.8160 (m) cc_final: 0.7943 (m) REVERT: R 506 MET cc_start: 0.8380 (tpp) cc_final: 0.7811 (mmp) outliers start: 23 outliers final: 13 residues processed: 98 average time/residue: 1.2485 time to fit residues: 130.7486 Evaluate side-chains 94 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 216 ASN Chi-restraints excluded: chain L residue 164 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 108 MET Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 251 SER Chi-restraints excluded: chain R residue 307 LYS Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 201 GLN N 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8637 Z= 0.203 Angle : 0.564 7.247 11733 Z= 0.305 Chirality : 0.043 0.215 1318 Planarity : 0.005 0.055 1477 Dihedral : 6.125 70.096 1218 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.53 % Allowed : 11.44 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.57 (0.26), residues: 1091 helix: 1.46 (0.29), residues: 360 sheet: 1.20 (0.32), residues: 286 loop : -1.11 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 178 HIS 0.007 0.001 HIS H 110 PHE 0.015 0.001 PHE R 526 TYR 0.021 0.001 TYR R 160 ARG 0.006 0.000 ARG R 164 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: H 47 LYS cc_start: 0.8257 (mtmt) cc_final: 0.8013 (mtpt) REVERT: H 54 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.7818 (t80) REVERT: N 28 ARG cc_start: 0.7434 (mmt90) cc_final: 0.7110 (mmt-90) REVERT: N 58 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7732 (mt) REVERT: N 108 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7239 (ttp) REVERT: R 254 GLN cc_start: 0.7780 (tp40) cc_final: 0.7537 (tp40) REVERT: R 500 SER cc_start: 0.8145 (m) cc_final: 0.7924 (m) REVERT: R 506 MET cc_start: 0.8413 (tpp) cc_final: 0.7579 (mmp) outliers start: 23 outliers final: 14 residues processed: 98 average time/residue: 1.2199 time to fit residues: 127.8229 Evaluate side-chains 101 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 216 ASN Chi-restraints excluded: chain L residue 164 SER Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 108 MET Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 251 SER Chi-restraints excluded: chain R residue 307 LYS Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 0.0970 chunk 8 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 ASN L 201 GLN N 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8637 Z= 0.167 Angle : 0.529 7.043 11733 Z= 0.285 Chirality : 0.042 0.195 1318 Planarity : 0.004 0.054 1477 Dihedral : 5.495 67.336 1218 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.75 % Allowed : 12.21 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.70 (0.27), residues: 1091 helix: 1.63 (0.29), residues: 360 sheet: 1.03 (0.30), residues: 312 loop : -1.02 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 178 HIS 0.006 0.001 HIS H 110 PHE 0.013 0.001 PHE R 327 TYR 0.021 0.001 TYR R 160 ARG 0.004 0.000 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 87 time to evaluate : 0.956 Fit side-chains REVERT: H 47 LYS cc_start: 0.8290 (mtmt) cc_final: 0.8031 (mtpt) REVERT: H 93 GLU cc_start: 0.7329 (mp0) cc_final: 0.7104 (mp0) REVERT: N 28 ARG cc_start: 0.7393 (mmt90) cc_final: 0.7070 (mmt-90) REVERT: N 58 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7603 (mt) REVERT: N 108 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7297 (ttp) REVERT: R 118 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6886 (m-30) REVERT: R 500 SER cc_start: 0.8146 (m) cc_final: 0.7928 (m) REVERT: R 534 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7257 (mt-10) REVERT: K 20 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7350 (mp) outliers start: 25 outliers final: 13 residues processed: 100 average time/residue: 1.2072 time to fit residues: 129.0722 Evaluate side-chains 102 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 216 ASN Chi-restraints excluded: chain L residue 164 SER Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 108 MET Chi-restraints excluded: chain R residue 118 ASP Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 152 MET Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 0.0030 chunk 87 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 ASN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8637 Z= 0.213 Angle : 0.563 6.756 11733 Z= 0.304 Chirality : 0.043 0.198 1318 Planarity : 0.005 0.055 1477 Dihedral : 5.469 66.881 1218 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.53 % Allowed : 13.31 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.71 (0.27), residues: 1091 helix: 1.57 (0.29), residues: 359 sheet: 1.08 (0.30), residues: 312 loop : -0.98 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 178 HIS 0.007 0.001 HIS H 110 PHE 0.014 0.001 PHE R 327 TYR 0.022 0.001 TYR R 160 ARG 0.003 0.000 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 0.846 Fit side-chains REVERT: H 47 LYS cc_start: 0.8239 (mtmt) cc_final: 0.7987 (mtpt) REVERT: H 54 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.7903 (t80) REVERT: H 93 GLU cc_start: 0.7370 (mp0) cc_final: 0.7143 (mp0) REVERT: L 6 MET cc_start: 0.8451 (mtm) cc_final: 0.7667 (mtm) REVERT: N 28 ARG cc_start: 0.7375 (mmt90) cc_final: 0.7073 (mmt-90) REVERT: N 58 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7656 (mt) REVERT: N 108 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7361 (ttp) REVERT: R 118 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6960 (m-30) REVERT: R 254 GLN cc_start: 0.7473 (tp40) cc_final: 0.7199 (tm-30) REVERT: R 500 SER cc_start: 0.8161 (m) cc_final: 0.7947 (m) REVERT: K 20 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7336 (mp) outliers start: 23 outliers final: 17 residues processed: 99 average time/residue: 1.2412 time to fit residues: 131.1307 Evaluate side-chains 106 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 216 ASN Chi-restraints excluded: chain L residue 164 SER Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 108 MET Chi-restraints excluded: chain R residue 118 ASP Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 152 MET Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 271 MET Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 83 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.0370 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 51 optimal weight: 0.2980 chunk 9 optimal weight: 0.4980 chunk 81 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 0.0870 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 ASN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8637 Z= 0.134 Angle : 0.501 7.000 11733 Z= 0.268 Chirality : 0.041 0.165 1318 Planarity : 0.004 0.054 1477 Dihedral : 5.205 65.347 1218 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.76 % Allowed : 14.41 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.82 (0.27), residues: 1091 helix: 1.82 (0.29), residues: 360 sheet: 0.90 (0.30), residues: 314 loop : -0.87 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 178 HIS 0.005 0.001 HIS H 110 PHE 0.011 0.001 PHE R 151 TYR 0.022 0.001 TYR R 160 ARG 0.003 0.000 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.947 Fit side-chains REVERT: H 54 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.7795 (t80) REVERT: H 93 GLU cc_start: 0.7331 (mp0) cc_final: 0.7125 (mp0) REVERT: L 6 MET cc_start: 0.8396 (mtm) cc_final: 0.7665 (mtm) REVERT: N 28 ARG cc_start: 0.7260 (mmt90) cc_final: 0.7028 (mmt-90) REVERT: N 58 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7487 (mt) REVERT: N 108 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7495 (ttp) REVERT: R 118 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6718 (m-30) REVERT: R 254 GLN cc_start: 0.7577 (tp40) cc_final: 0.7239 (tm-30) REVERT: R 500 SER cc_start: 0.8152 (m) cc_final: 0.7933 (m) REVERT: K 20 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7343 (mp) outliers start: 16 outliers final: 10 residues processed: 97 average time/residue: 1.2158 time to fit residues: 126.2038 Evaluate side-chains 98 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 216 ASN Chi-restraints excluded: chain L residue 164 SER Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 108 MET Chi-restraints excluded: chain R residue 118 ASP Chi-restraints excluded: chain R residue 152 MET Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 51.0716 > 50: distance: 57 - 62: 12.103 distance: 58 - 83: 5.598 distance: 62 - 63: 5.887 distance: 63 - 64: 16.700 distance: 63 - 66: 14.937 distance: 64 - 65: 8.276 distance: 64 - 67: 20.776 distance: 65 - 91: 9.047 distance: 67 - 68: 27.404 distance: 68 - 69: 8.508 distance: 68 - 71: 22.909 distance: 69 - 70: 6.744 distance: 69 - 75: 16.054 distance: 70 - 99: 12.539 distance: 71 - 72: 21.621 distance: 72 - 73: 42.709 distance: 72 - 74: 17.250 distance: 75 - 76: 6.816 distance: 76 - 77: 5.985 distance: 76 - 79: 7.188 distance: 77 - 83: 3.238 distance: 78 - 111: 11.087 distance: 79 - 80: 11.424 distance: 79 - 81: 12.799 distance: 80 - 82: 24.938 distance: 83 - 84: 3.503 distance: 84 - 85: 4.768 distance: 84 - 87: 4.226 distance: 85 - 86: 4.081 distance: 85 - 91: 3.267 distance: 87 - 88: 6.911 distance: 88 - 89: 3.467 distance: 88 - 90: 7.898 distance: 91 - 92: 5.627 distance: 92 - 93: 8.478 distance: 92 - 95: 5.197 distance: 93 - 94: 4.891 distance: 93 - 99: 4.186 distance: 95 - 96: 10.452 distance: 96 - 97: 7.429 distance: 97 - 98: 8.893 distance: 99 - 100: 11.484 distance: 100 - 101: 7.370 distance: 100 - 103: 7.401 distance: 101 - 102: 11.036 distance: 101 - 111: 12.677 distance: 103 - 104: 14.063 distance: 104 - 105: 5.119 distance: 104 - 106: 4.983 distance: 105 - 107: 14.004 distance: 106 - 108: 7.665 distance: 107 - 109: 4.164 distance: 108 - 109: 9.119 distance: 109 - 110: 11.758 distance: 111 - 112: 5.598 distance: 112 - 113: 5.566 distance: 112 - 115: 9.227 distance: 113 - 114: 11.369 distance: 113 - 118: 11.557 distance: 115 - 116: 8.974 distance: 115 - 117: 10.288 distance: 118 - 119: 14.473 distance: 119 - 120: 23.077 distance: 119 - 122: 17.660 distance: 120 - 121: 11.372 distance: 120 - 125: 21.983 distance: 122 - 123: 15.318 distance: 122 - 124: 23.965 distance: 125 - 126: 18.266 distance: 126 - 127: 16.525 distance: 126 - 129: 3.756 distance: 127 - 128: 6.086 distance: 127 - 133: 8.366 distance: 129 - 130: 19.159 distance: 129 - 131: 13.282 distance: 130 - 132: 14.438 distance: 133 - 134: 6.186 distance: 133 - 139: 11.092 distance: 134 - 135: 3.297 distance: 134 - 137: 18.771 distance: 135 - 136: 4.625 distance: 135 - 140: 6.093 distance: 137 - 138: 21.021 distance: 138 - 139: 17.486