Starting phenix.real_space_refine (version: dev) on Sun Mar 12 08:34:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnj_34166/03_2023/8gnj_34166_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnj_34166/03_2023/8gnj_34166.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnj_34166/03_2023/8gnj_34166_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnj_34166/03_2023/8gnj_34166_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnj_34166/03_2023/8gnj_34166_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnj_34166/03_2023/8gnj_34166.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnj_34166/03_2023/8gnj_34166.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnj_34166/03_2023/8gnj_34166_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnj_34166/03_2023/8gnj_34166_updated.pdb" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.015 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 Process input model Symmetric amino acids flipped Residue "A GLU 101": "OE1" <-> "OE2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "A GLU 469": "OE1" <-> "OE2" Residue "A GLU 472": "OE1" <-> "OE2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "B ARG 570": "NH1" <-> "NH2" Residue "B GLU 596": "OE1" <-> "OE2" Residue "B GLU 604": "OE1" <-> "OE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 689": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 5832 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3821 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 16, 'TRANS': 475} Chain: "B" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1125 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "C" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.96, per 1000 atoms: 0.68 Number of scatterers: 5832 At special positions: 0 Unit cell: (92.536, 93.612, 117.284, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 1 15.00 O 1091 8.00 N 1042 7.00 C 3670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 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: 2.28 Conformation dependent library (CDL) restraints added in 883.9 milliseconds 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 3 sheets defined 50.8% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 59 through 79 removed outlier: 3.514A pdb=" N LEU A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Proline residue: A 70 - end of helix removed outlier: 3.917A pdb=" N GLN A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLN A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 104 removed outlier: 4.684A pdb=" N GLN A 97 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 101 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 102 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 122 removed outlier: 3.673A pdb=" N GLN A 114 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG A 121 " --> pdb=" O CYS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 139 through 150 removed outlier: 4.029A pdb=" N ARG A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 4.115A pdb=" N ASP A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ARG A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 172 removed outlier: 3.544A pdb=" N LEU A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.922A pdb=" N ARG A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 220 through 236 Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.942A pdb=" N VAL A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 258 No H-bonds generated for 'chain 'A' and resid 255 through 258' Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.578A pdb=" N THR A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 287 No H-bonds generated for 'chain 'A' and resid 284 through 287' Processing helix chain 'A' and resid 293 through 302 removed outlier: 4.508A pdb=" N GLU A 297 " --> pdb=" O ALA A 294 " (cutoff:3.500A) Proline residue: A 298 - end of helix Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 339 through 357 removed outlier: 3.606A pdb=" N ALA A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 removed outlier: 3.662A pdb=" N SER A 366 " --> pdb=" O LYS A 363 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A 367 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 378 Processing helix chain 'A' and resid 384 through 397 Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 414 through 423 Processing helix chain 'A' and resid 427 through 435 removed outlier: 3.803A pdb=" N CYS A 430 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU A 431 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 433 " --> pdb=" O CYS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 443 No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 460 through 476 removed outlier: 4.052A pdb=" N GLU A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 475 " --> pdb=" O THR A 471 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 494 removed outlier: 3.747A pdb=" N LEU A 494 " --> pdb=" O TRP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 508 removed outlier: 3.568A pdb=" N ARG A 499 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR A 503 " --> pdb=" O GLN A 500 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER A 507 " --> pdb=" O GLY A 504 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N CYS A 508 " --> pdb=" O LEU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 517 No H-bonds generated for 'chain 'A' and resid 515 through 517' Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 532 through 543 Processing helix chain 'B' and resid 575 through 587 removed outlier: 3.852A pdb=" N HIS B 587 " --> pdb=" O HIS B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 613 Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 673 through 677 removed outlier: 3.716A pdb=" N THR B 677 " --> pdb=" O ALA B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 695 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing sheet with id= A, first strand: chain 'B' and resid 564 through 567 removed outlier: 6.653A pdb=" N ASN B 616 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N SER B 567 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 618 " --> pdb=" O SER B 567 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 654 " --> pdb=" O LEU B 619 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 5 through 8 removed outlier: 3.633A pdb=" N SER C 8 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 11 through 13 removed outlier: 3.783A pdb=" N ALA C 50 " --> pdb=" O TRP C 37 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ARG C 39 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL C 48 " --> pdb=" O ARG C 39 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 531 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: 1.65 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1662 1.33 - 1.45: 1102 1.45 - 1.58: 3127 1.58 - 1.70: 1 1.70 - 1.82: 38 Bond restraints: 5930 Sorted by residual: bond pdb=" C3R NMN A1001 " pdb=" C4R NMN A1001 " ideal model delta sigma weight residual 1.304 1.532 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C4R NMN A1001 " pdb=" O4R NMN A1001 " ideal model delta sigma weight residual 1.615 1.442 0.173 2.00e-02 2.50e+03 7.50e+01 bond pdb=" C7 NMN A1001 " pdb=" N7 NMN A1001 " ideal model delta sigma weight residual 1.451 1.322 0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" C1R NMN A1001 " pdb=" O4R NMN A1001 " ideal model delta sigma weight residual 1.305 1.409 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C SER A 319 " pdb=" O SER A 319 " ideal model delta sigma weight residual 1.236 1.284 -0.047 1.16e-02 7.43e+03 1.65e+01 ... (remaining 5925 not shown) Histogram of bond angle deviations from ideal: 97.10 - 104.49: 78 104.49 - 111.88: 2685 111.88 - 119.28: 2339 119.28 - 126.67: 2838 126.67 - 134.07: 86 Bond angle restraints: 8026 Sorted by residual: angle pdb=" N LYS A 80 " pdb=" CA LYS A 80 " pdb=" C LYS A 80 " ideal model delta sigma weight residual 113.20 105.31 7.89 1.21e+00 6.83e-01 4.25e+01 angle pdb=" N PRO A 549 " pdb=" CA PRO A 549 " pdb=" CB PRO A 549 " ideal model delta sigma weight residual 103.00 97.73 5.27 1.10e+00 8.26e-01 2.29e+01 angle pdb=" C GLU A 284 " pdb=" N ARG A 285 " pdb=" CA ARG A 285 " ideal model delta sigma weight residual 121.58 112.70 8.88 1.95e+00 2.63e-01 2.07e+01 angle pdb=" N LEU A 79 " pdb=" CA LEU A 79 " pdb=" C LEU A 79 " ideal model delta sigma weight residual 112.23 106.58 5.65 1.26e+00 6.30e-01 2.01e+01 angle pdb=" N HIS A 547 " pdb=" CA HIS A 547 " pdb=" C HIS A 547 " ideal model delta sigma weight residual 111.54 105.63 5.91 1.36e+00 5.41e-01 1.89e+01 ... (remaining 8021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 3224 17.51 - 35.02: 281 35.02 - 52.53: 57 52.53 - 70.04: 25 70.04 - 87.55: 8 Dihedral angle restraints: 3595 sinusoidal: 1452 harmonic: 2143 Sorted by residual: dihedral pdb=" CA VAL A 95 " pdb=" C VAL A 95 " pdb=" N PHE A 96 " pdb=" CA PHE A 96 " ideal model delta harmonic sigma weight residual 180.00 -153.87 -26.13 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA GLY A 84 " pdb=" C GLY A 84 " pdb=" N ALA A 85 " pdb=" CA ALA A 85 " ideal model delta harmonic sigma weight residual 180.00 154.85 25.15 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA LYS C 76 " pdb=" C LYS C 76 " pdb=" N ASN C 77 " pdb=" CA ASN C 77 " ideal model delta harmonic sigma weight residual -180.00 -161.95 -18.05 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 3592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 736 0.085 - 0.170: 152 0.170 - 0.256: 25 0.256 - 0.341: 2 0.341 - 0.426: 1 Chirality restraints: 916 Sorted by residual: chirality pdb=" CG LEU A 148 " pdb=" CB LEU A 148 " pdb=" CD1 LEU A 148 " pdb=" CD2 LEU A 148 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CA LYS A 80 " pdb=" N LYS A 80 " pdb=" C LYS A 80 " pdb=" CB LYS A 80 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA THR A 318 " pdb=" N THR A 318 " pdb=" C THR A 318 " pdb=" CB THR A 318 " both_signs ideal model delta sigma weight residual False 2.53 2.82 -0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 913 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 99 " 0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C VAL A 99 " -0.073 2.00e-02 2.50e+03 pdb=" O VAL A 99 " 0.027 2.00e-02 2.50e+03 pdb=" N GLU A 100 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 545 " -0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C MET A 545 " 0.069 2.00e-02 2.50e+03 pdb=" O MET A 545 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU A 546 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 63 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C ASP A 63 " 0.060 2.00e-02 2.50e+03 pdb=" O ASP A 63 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA A 64 " -0.020 2.00e-02 2.50e+03 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 34 2.43 - 3.05: 3610 3.05 - 3.66: 8998 3.66 - 4.28: 12663 4.28 - 4.90: 20637 Nonbonded interactions: 45942 Sorted by model distance: nonbonded pdb=" NH1 ARG A 216 " pdb=" NE2 GLN B 688 " model vdw 1.811 3.200 nonbonded pdb=" OE2 GLU A 400 " pdb=" O VAL A 401 " model vdw 2.030 3.040 nonbonded pdb=" CD1 LEU A 76 " pdb=" NZ LYS A 80 " model vdw 2.184 3.540 nonbonded pdb=" OG1 THR A 447 " pdb=" OE1 GLU A 450 " model vdw 2.200 2.440 nonbonded pdb=" OD1 ASP A 441 " pdb=" OH TYR A 503 " model vdw 2.258 2.440 ... (remaining 45937 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 28 5.16 5 C 3670 2.51 5 N 1042 2.21 5 O 1091 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 7.000 Check model and map are aligned: 0.080 Process input model: 19.120 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 0.012 0.228 5930 Z= 0.820 Angle : 1.338 14.332 8026 Z= 0.718 Chirality : 0.072 0.426 916 Planarity : 0.008 0.059 1040 Dihedral : 15.382 87.554 2208 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 0.00 % 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: -3.73 (0.26), residues: 740 helix: -3.26 (0.18), residues: 384 sheet: -0.37 (0.71), residues: 56 loop : -1.50 (0.34), residues: 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 0.697 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.2639 time to fit residues: 75.0310 Evaluate side-chains 176 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.658 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 5930 Z= 0.262 Angle : 0.727 9.761 8026 Z= 0.355 Chirality : 0.044 0.219 916 Planarity : 0.005 0.046 1040 Dihedral : 5.157 26.044 816 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 2.74 % 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: -2.33 (0.29), residues: 740 helix: -1.95 (0.23), residues: 384 sheet: -0.47 (0.61), residues: 67 loop : -0.93 (0.37), residues: 289 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 189 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 196 average time/residue: 0.2280 time to fit residues: 55.2289 Evaluate side-chains 183 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 0.696 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0629 time to fit residues: 2.4174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 18 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 269 HIS ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 5930 Z= 0.251 Angle : 0.679 10.286 8026 Z= 0.328 Chirality : 0.043 0.187 916 Planarity : 0.004 0.040 1040 Dihedral : 4.891 20.892 816 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 3.06 % 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: -1.53 (0.30), residues: 740 helix: -1.21 (0.26), residues: 376 sheet: -0.09 (0.62), residues: 67 loop : -0.70 (0.37), residues: 297 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 183 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 187 average time/residue: 0.2286 time to fit residues: 52.6353 Evaluate side-chains 175 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 166 time to evaluate : 0.718 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0641 time to fit residues: 2.0410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 232 ASN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 5930 Z= 0.266 Angle : 0.675 9.352 8026 Z= 0.324 Chirality : 0.043 0.191 916 Planarity : 0.004 0.041 1040 Dihedral : 4.883 30.600 816 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 1.13 % 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: -1.28 (0.30), residues: 740 helix: -0.98 (0.26), residues: 375 sheet: 0.00 (0.62), residues: 67 loop : -0.63 (0.36), residues: 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 173 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 177 average time/residue: 0.2348 time to fit residues: 51.4570 Evaluate side-chains 166 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 163 time to evaluate : 0.733 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0583 time to fit residues: 1.3301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 4.9990 chunk 40 optimal weight: 0.1980 chunk 1 optimal weight: 0.9980 chunk 53 optimal weight: 0.0370 chunk 29 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 0 optimal weight: 0.6980 chunk 36 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 5930 Z= 0.181 Angle : 0.632 8.500 8026 Z= 0.305 Chirality : 0.042 0.195 916 Planarity : 0.004 0.041 1040 Dihedral : 4.687 30.228 816 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 1.61 % 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: 740 helix: -0.68 (0.27), residues: 374 sheet: 0.35 (0.69), residues: 57 loop : -0.55 (0.35), residues: 309 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 170 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 174 average time/residue: 0.2380 time to fit residues: 51.3845 Evaluate side-chains 165 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 163 time to evaluate : 0.711 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0586 time to fit residues: 1.1675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/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-dev-4893/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-4893/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-4893/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-4893/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-4893/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-4893/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-4893/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/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-4893/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-4893/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-4893/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: 50.9961 > 50: distance: 18 - 155: 17.562 distance: 21 - 152: 4.571 distance: 36 - 138: 17.987 distance: 39 - 135: 13.139 distance: 84 - 146: 11.422 distance: 87 - 143: 18.791 distance: 97 - 126: 20.122 distance: 100 - 123: 10.774 distance: 118 - 123: 8.019 distance: 123 - 124: 13.031 distance: 124 - 125: 23.644 distance: 124 - 127: 12.124 distance: 125 - 126: 8.678 distance: 125 - 135: 14.224 distance: 127 - 128: 13.966 distance: 128 - 129: 10.759 distance: 128 - 130: 11.128 distance: 129 - 131: 6.446 distance: 130 - 132: 18.627 distance: 131 - 133: 4.367 distance: 132 - 133: 6.884 distance: 133 - 134: 4.307 distance: 135 - 136: 18.108 distance: 136 - 137: 32.325 distance: 136 - 139: 25.998 distance: 137 - 138: 31.632 distance: 137 - 143: 32.351 distance: 139 - 140: 18.272 distance: 140 - 141: 7.882 distance: 140 - 142: 16.064 distance: 143 - 144: 16.928 distance: 144 - 145: 12.841 distance: 144 - 147: 3.871 distance: 145 - 146: 5.166 distance: 145 - 152: 8.580 distance: 147 - 148: 18.926 distance: 148 - 149: 13.565 distance: 149 - 150: 13.393 distance: 149 - 151: 10.522 distance: 152 - 153: 15.227 distance: 153 - 154: 18.746 distance: 153 - 156: 17.232 distance: 154 - 155: 18.137 distance: 154 - 160: 14.670 distance: 156 - 157: 13.053 distance: 157 - 158: 8.669 distance: 158 - 159: 3.905 distance: 160 - 161: 18.466 distance: 161 - 162: 27.633 distance: 161 - 164: 30.475 distance: 162 - 163: 12.977 distance: 162 - 168: 35.212 distance: 164 - 165: 15.217 distance: 165 - 166: 22.113 distance: 165 - 167: 12.069 distance: 168 - 169: 10.762 distance: 169 - 170: 10.970 distance: 169 - 172: 13.477 distance: 170 - 171: 29.501 distance: 170 - 174: 26.014 distance: 172 - 173: 21.938 distance: 174 - 175: 23.742 distance: 175 - 176: 22.095 distance: 175 - 178: 22.972 distance: 176 - 177: 7.478 distance: 176 - 182: 9.874 distance: 178 - 179: 16.234 distance: 179 - 180: 5.685 distance: 179 - 181: 5.967 distance: 182 - 183: 20.289 distance: 183 - 184: 12.844 distance: 183 - 186: 8.825 distance: 184 - 185: 17.512 distance: 184 - 191: 21.756 distance: 186 - 187: 13.437 distance: 187 - 188: 6.212 distance: 188 - 189: 7.238 distance: 189 - 190: 9.960 distance: 191 - 192: 15.873 distance: 191 - 197: 19.402 distance: 192 - 193: 20.642 distance: 192 - 195: 8.856 distance: 193 - 194: 40.977 distance: 193 - 198: 26.817 distance: 195 - 196: 8.990 distance: 196 - 197: 11.198 distance: 198 - 199: 22.022 distance: 199 - 200: 3.521 distance: 199 - 202: 5.813 distance: 200 - 201: 14.624 distance: 200 - 207: 5.788 distance: 202 - 203: 13.999 distance: 203 - 204: 10.874 distance: 204 - 205: 8.005 distance: 204 - 206: 9.437