Starting phenix.real_space_refine on Sun Dec 10 03:07:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2u_27846/12_2023/8e2u_27846.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2u_27846/12_2023/8e2u_27846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2u_27846/12_2023/8e2u_27846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2u_27846/12_2023/8e2u_27846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2u_27846/12_2023/8e2u_27846.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2u_27846/12_2023/8e2u_27846.pdb" } resolution = 3.48 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= 0.001 sd= 0.089 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 S 35 5.16 5 C 4164 2.51 5 N 1144 2.21 5 O 1304 1.98 5 H 6581 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ASP 92": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13228 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6728 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 15, 'TRANS': 423} Chain: "L" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3159 Classifications: {'peptide': 216} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 199} Chain: "H" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3341 Classifications: {'peptide': 225} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Time building chain proxies: 6.07, per 1000 atoms: 0.46 Number of scatterers: 13228 At special positions: 0 Unit cell: (74.37, 117.66, 142.08, 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 35 16.00 O 1304 8.00 N 1144 7.00 C 4164 6.00 H 6581 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 301 " distance=1.62 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS L 212 " - pdb=" SG CYS H 216 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 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: 9.60 Conformation dependent library (CDL) restraints added in 1.4 seconds 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1622 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 16 sheets defined 15.6% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 65 through 89 removed outlier: 3.602A pdb=" N ASP A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.560A pdb=" N GLY A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.790A pdb=" N THR A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 141 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 197 through 210 removed outlier: 3.558A pdb=" N LEU A 201 " --> pdb=" O ASN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.590A pdb=" N CYS A 350 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 351 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 129 removed outlier: 3.588A pdb=" N ALA L 128 " --> pdb=" O GLU L 125 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN L 129 " --> pdb=" O LEU L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 189 removed outlier: 3.585A pdb=" N HIS L 189 " --> pdb=" O GLN L 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.646A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 273 through 278 removed outlier: 3.928A pdb=" N GLY A 42 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLY A 277 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ARG A 40 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY A 34 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS A 283 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR A 320 " --> pdb=" O TRP A 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 333 through 336 removed outlier: 6.115A pdb=" N GLU A 21 " --> pdb=" O HIS A 435 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE A 437 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR A 23 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 150 removed outlier: 3.544A pdb=" N ALA A 159 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL A 47 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A 269 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 267 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SER A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL A 262 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE A 268 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 375 removed outlier: 3.511A pdb=" N MET A 372 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 401 through 402 removed outlier: 3.925A pdb=" N LYS A 401 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.721A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.715A pdb=" N VAL L 97 " --> pdb=" O SER L 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AA9, first strand: chain 'L' and resid 115 through 119 removed outlier: 4.150A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TYR L 173 " --> pdb=" O ASP L 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 154 through 156 removed outlier: 4.231A pdb=" N TRP L 149 " --> pdb=" O VAL L 156 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR L 146 " --> pdb=" O THR L 197 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 192 through 193 Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.903A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.793A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 96 through 97 Processing sheet with id=AB6, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.537A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL H 181 " --> pdb=" O HIS H 164 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS H 164 " --> pdb=" O VAL H 181 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 150 through 153 removed outlier: 3.586A pdb=" N THR H 151 " --> pdb=" O ASN H 199 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS H 209 " --> pdb=" O CYS H 196 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL H 198 " --> pdb=" O VAL H 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL H 207 " --> pdb=" O VAL H 198 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 534 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: 4.38 Time building geometry restraints manager: 10.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6581 1.04 - 1.24: 909 1.24 - 1.44: 1968 1.44 - 1.64: 3857 1.64 - 1.84: 44 Bond restraints: 13359 Sorted by residual: bond pdb=" C ASN H 82A" pdb=" O ASN H 82A" ideal model delta sigma weight residual 1.234 1.135 0.098 1.22e-02 6.72e+03 6.50e+01 bond pdb=" C ILE H 100 " pdb=" O ILE H 100 " ideal model delta sigma weight residual 1.235 1.145 0.090 1.31e-02 5.83e+03 4.70e+01 bond pdb=" N PRO A 452 " pdb=" CD PRO A 452 " ideal model delta sigma weight residual 1.473 1.406 0.067 1.40e-02 5.10e+03 2.29e+01 bond pdb=" C PRO H 147 " pdb=" O PRO H 147 " ideal model delta sigma weight residual 1.232 1.178 0.054 1.25e-02 6.40e+03 1.89e+01 bond pdb=" C GLN L 89 " pdb=" O GLN L 89 " ideal model delta sigma weight residual 1.235 1.182 0.053 1.28e-02 6.10e+03 1.71e+01 ... (remaining 13354 not shown) Histogram of bond angle deviations from ideal: 92.02 - 100.43: 6 100.43 - 108.84: 4501 108.84 - 117.24: 13386 117.24 - 125.65: 6096 125.65 - 134.06: 160 Bond angle restraints: 24149 Sorted by residual: angle pdb=" CA ILE H 100 " pdb=" C ILE H 100 " pdb=" N SER H 100A" ideal model delta sigma weight residual 117.15 124.12 -6.97 7.80e-01 1.64e+00 7.98e+01 angle pdb=" CA ILE H 100 " pdb=" C ILE H 100 " pdb=" O ILE H 100 " ideal model delta sigma weight residual 120.80 113.33 7.47 8.90e-01 1.26e+00 7.04e+01 angle pdb=" N SER A 293 " pdb=" CA SER A 293 " pdb=" C SER A 293 " ideal model delta sigma weight residual 107.62 92.02 15.60 1.97e+00 2.58e-01 6.27e+01 angle pdb=" CA PRO H 147 " pdb=" C PRO H 147 " pdb=" O PRO H 147 " ideal model delta sigma weight residual 121.96 112.91 9.05 1.23e+00 6.61e-01 5.41e+01 angle pdb=" CA PRO H 147 " pdb=" C PRO H 147 " pdb=" N GLU H 148 " ideal model delta sigma weight residual 114.74 122.32 -7.58 1.03e+00 9.43e-01 5.41e+01 ... (remaining 24144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5631 17.72 - 35.43: 383 35.43 - 53.15: 136 53.15 - 70.86: 33 70.86 - 88.58: 13 Dihedral angle restraints: 6196 sinusoidal: 3310 harmonic: 2886 Sorted by residual: dihedral pdb=" CB CYS A 292 " pdb=" SG CYS A 292 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 39.54 53.46 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS L 212 " pdb=" SG CYS L 212 " pdb=" SG CYS H 216 " pdb=" CB CYS H 216 " ideal model delta sinusoidal sigma weight residual 93.00 140.90 -47.90 1 1.00e+01 1.00e-02 3.16e+01 dihedral pdb=" CB CYS H 140 " pdb=" SG CYS H 140 " pdb=" SG CYS H 196 " pdb=" CB CYS H 196 " ideal model delta sinusoidal sigma weight residual 93.00 135.96 -42.96 1 1.00e+01 1.00e-02 2.57e+01 ... (remaining 6193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 754 0.049 - 0.098: 224 0.098 - 0.148: 66 0.148 - 0.197: 14 0.197 - 0.246: 2 Chirality restraints: 1060 Sorted by residual: chirality pdb=" CA GLN L 168 " pdb=" N GLN L 168 " pdb=" C GLN L 168 " pdb=" CB GLN L 168 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ASP L 152 " pdb=" N ASP L 152 " pdb=" C ASP L 152 " pdb=" CB ASP L 152 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PHE H 146 " pdb=" N PHE H 146 " pdb=" C PHE H 146 " pdb=" CB PHE H 146 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.53e-01 ... (remaining 1057 not shown) Planarity restraints: 2020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN H 82A" 0.035 2.00e-02 2.50e+03 4.29e-01 2.76e+03 pdb=" CG ASN H 82A" 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN H 82A" -0.038 2.00e-02 2.50e+03 pdb=" ND2 ASN H 82A" -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN H 82A" -0.745 2.00e-02 2.50e+03 pdb="HD22 ASN H 82A" 0.739 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN L 168 " 0.164 2.00e-02 2.50e+03 4.10e-01 2.52e+03 pdb=" CD GLN L 168 " -0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN L 168 " -0.159 2.00e-02 2.50e+03 pdb=" NE2 GLN L 168 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN L 168 " -0.686 2.00e-02 2.50e+03 pdb="HE22 GLN L 168 " 0.695 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 455 " 0.165 2.00e-02 2.50e+03 4.10e-01 2.52e+03 pdb=" CD GLN A 455 " -0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN A 455 " -0.157 2.00e-02 2.50e+03 pdb=" NE2 GLN A 455 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 455 " 0.697 2.00e-02 2.50e+03 pdb="HE22 GLN A 455 " -0.684 2.00e-02 2.50e+03 ... (remaining 2017 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.02: 180 2.02 - 2.67: 18621 2.67 - 3.31: 35296 3.31 - 3.96: 45513 3.96 - 4.60: 70091 Nonbonded interactions: 169701 Sorted by model distance: nonbonded pdb=" OE2 GLU A 21 " pdb=" HG SER A 376 " model vdw 1.380 1.850 nonbonded pdb=" HG1 THR L 146 " pdb=" HG1 THR L 197 " model vdw 1.436 2.100 nonbonded pdb=" O CYS A 60 " pdb=" HZ3 LYS A 68 " model vdw 1.437 1.850 nonbonded pdb=" HH TYR A 23 " pdb=" O CYS A 407 " model vdw 1.526 1.850 nonbonded pdb=" OE1 GLU A 21 " pdb=" HH TYR A 409 " model vdw 1.542 1.850 ... (remaining 169696 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: 1.400 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: 0.210 Extract box with map and model: 7.500 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 41.630 Find NCS groups from input model: 0.240 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 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 : 0.006 0.098 6778 Z= 0.353 Angle : 0.971 15.600 9212 Z= 0.614 Chirality : 0.052 0.246 1060 Planarity : 0.007 0.112 1186 Dihedral : 14.007 88.580 2459 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.24 % Favored : 91.42 % Rotamer: Outliers : 0.94 % Allowed : 1.08 % Favored : 97.98 % 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: -2.08 (0.28), residues: 874 helix: -1.75 (0.43), residues: 137 sheet: 0.12 (0.36), residues: 258 loop : -2.21 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 100D HIS 0.006 0.001 HIS L 198 PHE 0.019 0.002 PHE A 446 TYR 0.037 0.002 TYR A 299 ARG 0.003 0.001 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.983 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 81 average time/residue: 0.2784 time to fit residues: 33.7385 Evaluate side-chains 60 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 1.006 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1934 time to fit residues: 1.6280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.3980 chunk 65 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.0970 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6778 Z= 0.202 Angle : 0.613 5.862 9212 Z= 0.324 Chirality : 0.046 0.163 1060 Planarity : 0.005 0.057 1186 Dihedral : 4.889 20.920 947 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.21 % Favored : 92.68 % Rotamer: Outliers : 0.40 % Allowed : 7.41 % Favored : 92.18 % 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: -1.71 (0.28), residues: 874 helix: -1.05 (0.47), residues: 131 sheet: 0.57 (0.34), residues: 272 loop : -2.33 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS L 34 PHE 0.010 0.001 PHE H 122 TYR 0.011 0.001 TYR L 49 ARG 0.002 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 66 average time/residue: 0.2841 time to fit residues: 28.6949 Evaluate side-chains 62 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.933 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1663 time to fit residues: 2.1068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6778 Z= 0.216 Angle : 0.568 5.212 9212 Z= 0.298 Chirality : 0.045 0.154 1060 Planarity : 0.004 0.051 1186 Dihedral : 4.764 19.551 947 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.12 % Favored : 91.76 % Rotamer: Outliers : 0.54 % Allowed : 8.76 % Favored : 90.70 % 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: -1.77 (0.28), residues: 874 helix: -0.88 (0.47), residues: 138 sheet: 0.27 (0.34), residues: 269 loop : -2.25 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.005 0.001 HIS H 35 PHE 0.012 0.001 PHE H 100E TYR 0.015 0.001 TYR L 49 ARG 0.002 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 68 average time/residue: 0.3014 time to fit residues: 30.1855 Evaluate side-chains 66 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.920 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1339 time to fit residues: 1.9597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6778 Z= 0.263 Angle : 0.576 5.188 9212 Z= 0.304 Chirality : 0.046 0.150 1060 Planarity : 0.004 0.052 1186 Dihedral : 4.829 20.528 947 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.24 % Favored : 91.65 % Rotamer: Outliers : 0.54 % Allowed : 10.24 % Favored : 89.22 % 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: -1.82 (0.28), residues: 874 helix: -0.78 (0.47), residues: 137 sheet: 0.23 (0.33), residues: 275 loop : -2.36 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.005 0.001 HIS H 35 PHE 0.015 0.001 PHE H 122 TYR 0.018 0.001 TYR L 49 ARG 0.003 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 71 average time/residue: 0.3002 time to fit residues: 31.4242 Evaluate side-chains 69 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 1.028 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.1516 time to fit residues: 2.4465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 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 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6778 Z= 0.223 Angle : 0.551 5.049 9212 Z= 0.288 Chirality : 0.045 0.146 1060 Planarity : 0.004 0.050 1186 Dihedral : 4.728 20.107 947 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.47 % Favored : 91.42 % Rotamer: Outliers : 0.67 % Allowed : 11.05 % Favored : 88.27 % 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: -1.80 (0.28), residues: 874 helix: -0.66 (0.48), residues: 138 sheet: 0.17 (0.33), residues: 275 loop : -2.32 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.011 0.001 PHE H 100E TYR 0.015 0.001 TYR L 49 ARG 0.003 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 72 average time/residue: 0.3334 time to fit residues: 34.4432 Evaluate side-chains 69 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 1.027 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.1635 time to fit residues: 2.4378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 0.0570 chunk 83 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 0.0000 chunk 80 optimal weight: 2.9990 overall best weight: 0.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6778 Z= 0.164 Angle : 0.521 5.229 9212 Z= 0.270 Chirality : 0.044 0.148 1060 Planarity : 0.004 0.048 1186 Dihedral : 4.538 18.590 947 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.55 % Favored : 92.33 % Rotamer: Outliers : 0.94 % Allowed : 11.19 % Favored : 87.87 % 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: -1.67 (0.28), residues: 874 helix: -0.50 (0.49), residues: 137 sheet: 0.33 (0.34), residues: 261 loop : -2.23 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.007 0.001 PHE H 100E TYR 0.009 0.001 TYR L 49 ARG 0.002 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 70 average time/residue: 0.3405 time to fit residues: 34.2498 Evaluate side-chains 72 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.968 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 7 average time/residue: 0.1520 time to fit residues: 3.2810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 6.9990 chunk 47 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 51 optimal weight: 0.0270 chunk 50 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6778 Z= 0.172 Angle : 0.521 5.167 9212 Z= 0.269 Chirality : 0.044 0.145 1060 Planarity : 0.004 0.047 1186 Dihedral : 4.453 18.632 947 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.35 % Favored : 91.53 % Rotamer: Outliers : 0.54 % Allowed : 11.73 % Favored : 87.74 % 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: -1.60 (0.28), residues: 874 helix: -0.45 (0.48), residues: 137 sheet: 0.39 (0.34), residues: 260 loop : -2.20 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.001 PHE H 100E TYR 0.010 0.001 TYR L 49 ARG 0.002 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 67 average time/residue: 0.3508 time to fit residues: 33.2963 Evaluate side-chains 70 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 1.018 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 4 average time/residue: 0.1538 time to fit residues: 2.4997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6778 Z= 0.254 Angle : 0.553 5.209 9212 Z= 0.289 Chirality : 0.045 0.145 1060 Planarity : 0.004 0.049 1186 Dihedral : 4.577 19.774 947 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.38 % Favored : 90.50 % Rotamer: Outliers : 0.54 % Allowed : 11.73 % Favored : 87.74 % 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: -1.80 (0.28), residues: 874 helix: -0.58 (0.47), residues: 141 sheet: 0.03 (0.32), residues: 278 loop : -2.28 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 100D HIS 0.005 0.001 HIS H 35 PHE 0.010 0.001 PHE H 100E TYR 0.018 0.001 TYR L 49 ARG 0.004 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 65 average time/residue: 0.3667 time to fit residues: 33.4232 Evaluate side-chains 65 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 1.035 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 4 average time/residue: 0.1496 time to fit residues: 2.4308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 81 optimal weight: 0.0030 chunk 49 optimal weight: 0.4980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6778 Z= 0.211 Angle : 0.539 5.170 9212 Z= 0.281 Chirality : 0.044 0.144 1060 Planarity : 0.004 0.046 1186 Dihedral : 4.545 19.527 947 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.92 % Favored : 90.96 % Rotamer: Outliers : 0.40 % Allowed : 12.53 % Favored : 87.06 % 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: -1.78 (0.28), residues: 874 helix: -0.51 (0.47), residues: 141 sheet: 0.04 (0.32), residues: 278 loop : -2.28 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 100D HIS 0.004 0.001 HIS H 35 PHE 0.010 0.001 PHE H 100E TYR 0.014 0.001 TYR L 49 ARG 0.002 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 63 average time/residue: 0.3648 time to fit residues: 32.2333 Evaluate side-chains 63 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.933 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.2962 time to fit residues: 2.4574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.0870 chunk 56 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 78 optimal weight: 0.0470 chunk 68 optimal weight: 0.1980 chunk 7 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 0.0470 chunk 20 optimal weight: 0.9990 overall best weight: 0.2354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 6778 Z= 0.145 Angle : 0.509 5.357 9212 Z= 0.262 Chirality : 0.044 0.148 1060 Planarity : 0.004 0.045 1186 Dihedral : 4.338 18.089 947 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.21 % Favored : 92.68 % Rotamer: Outliers : 0.40 % Allowed : 12.80 % Favored : 86.79 % 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: -1.52 (0.28), residues: 874 helix: -0.21 (0.49), residues: 137 sheet: 0.42 (0.34), residues: 259 loop : -2.19 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.006 0.001 PHE H 100E TYR 0.008 0.001 TYR A 409 ARG 0.002 0.000 ARG H 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 68 average time/residue: 0.3576 time to fit residues: 34.2706 Evaluate side-chains 66 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 1.052 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.1464 time to fit residues: 2.1458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.2746 > 50: distance: 70 - 82: 5.694 distance: 82 - 83: 6.987 distance: 82 - 90: 12.525 distance: 83 - 84: 16.451 distance: 83 - 86: 14.354 distance: 83 - 91: 16.824 distance: 84 - 85: 18.916 distance: 84 - 96: 14.280 distance: 86 - 87: 13.230 distance: 86 - 92: 9.674 distance: 86 - 93: 8.312 distance: 87 - 88: 6.975 distance: 87 - 89: 10.354 distance: 89 - 94: 11.427 distance: 89 - 95: 3.942 distance: 96 - 97: 21.941 distance: 96 - 101: 14.481 distance: 97 - 98: 27.256 distance: 97 - 100: 18.421 distance: 97 - 102: 18.557 distance: 98 - 99: 30.838 distance: 98 - 106: 17.622 distance: 100 - 103: 15.476 distance: 100 - 104: 13.867 distance: 106 - 107: 20.021 distance: 106 - 110: 27.341 distance: 107 - 108: 4.906 distance: 107 - 111: 32.239 distance: 107 - 112: 27.008 distance: 108 - 109: 6.505 distance: 108 - 113: 10.218 distance: 113 - 114: 15.514 distance: 113 - 120: 18.458 distance: 114 - 115: 34.494 distance: 114 - 117: 31.742 distance: 114 - 121: 17.701 distance: 115 - 116: 15.932 distance: 115 - 129: 14.886 distance: 117 - 118: 17.530 distance: 117 - 119: 27.587 distance: 117 - 122: 13.744 distance: 118 - 123: 32.821 distance: 118 - 124: 7.170 distance: 118 - 125: 19.985 distance: 119 - 126: 28.312 distance: 119 - 127: 9.910 distance: 119 - 128: 9.944 distance: 129 - 130: 26.802 distance: 129 - 138: 13.261 distance: 130 - 131: 18.623 distance: 130 - 133: 13.969 distance: 130 - 139: 19.971 distance: 131 - 132: 23.162 distance: 131 - 144: 17.376 distance: 133 - 134: 14.298 distance: 133 - 140: 15.602 distance: 133 - 141: 43.184 distance: 134 - 135: 23.935 distance: 134 - 142: 14.709 distance: 134 - 143: 23.558 distance: 135 - 136: 9.346 distance: 135 - 137: 8.169 distance: 144 - 145: 26.947 distance: 144 - 151: 22.353 distance: 145 - 146: 24.155 distance: 145 - 148: 37.354 distance: 145 - 152: 55.935 distance: 146 - 147: 33.510 distance: 146 - 158: 24.945 distance: 148 - 149: 16.156 distance: 148 - 150: 23.669 distance: 148 - 153: 20.899 distance: 149 - 154: 29.475 distance: 150 - 155: 24.215 distance: 150 - 156: 18.478 distance: 150 - 157: 41.695 distance: 158 - 159: 25.012 distance: 158 - 165: 35.460 distance: 159 - 160: 22.937 distance: 159 - 162: 18.802 distance: 159 - 166: 40.809 distance: 160 - 161: 12.632 distance: 160 - 172: 45.798 distance: 162 - 163: 30.772 distance: 162 - 164: 16.912 distance: 162 - 167: 18.536 distance: 163 - 168: 41.143 distance: 164 - 169: 11.536 distance: 164 - 170: 20.156 distance: 164 - 171: 36.409 distance: 172 - 173: 17.913 distance: 172 - 181: 37.484 distance: 173 - 174: 40.247 distance: 173 - 176: 47.580 distance: 173 - 182: 26.340 distance: 174 - 175: 39.677 distance: 174 - 194: 28.108 distance: 176 - 177: 41.601 distance: 176 - 183: 44.259 distance: 176 - 184: 19.552 distance: 177 - 178: 21.119 distance: 177 - 185: 28.264 distance: 177 - 186: 15.226 distance: 178 - 179: 9.071 distance: 178 - 187: 9.616 distance: 178 - 188: 9.168 distance: 179 - 180: 23.387 distance: 179 - 190: 31.020 distance: 180 - 192: 10.430 distance: 194 - 195: 43.862 distance: 194 - 200: 6.178 distance: 195 - 198: 4.125 distance: 195 - 201: 20.492 distance: 196 - 208: 40.459 distance: 198 - 199: 34.709 distance: 198 - 202: 16.264 distance: 198 - 203: 4.245 distance: 199 - 200: 20.635 distance: 199 - 204: 5.960 distance: 199 - 205: 22.197 distance: 200 - 206: 14.769 distance: 200 - 207: 33.315 distance: 208 - 209: 31.539 distance: 208 - 214: 16.458 distance: 208 - 256: 15.520 distance: 209 - 210: 35.410 distance: 209 - 212: 28.807 distance: 209 - 215: 18.569 distance: 210 - 211: 21.720 distance: 210 - 219: 9.760 distance: 211 - 253: 15.470 distance: 212 - 213: 22.885 distance: 212 - 217: 17.636 distance: 213 - 218: 3.432