Starting phenix.real_space_refine on Tue Sep 24 10:21:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk3_21224/09_2024/6vk3_21224.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk3_21224/09_2024/6vk3_21224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk3_21224/09_2024/6vk3_21224.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk3_21224/09_2024/6vk3_21224.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk3_21224/09_2024/6vk3_21224.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk3_21224/09_2024/6vk3_21224.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 4967 2.51 5 N 1303 2.21 5 O 1476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7784 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1906 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain breaks: 2 Chain: "A" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3060 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 369} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2818 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 10, 'TRANS': 339} Chain breaks: 2 Time building chain proxies: 4.46, per 1000 atoms: 0.57 Number of scatterers: 7784 At special positions: 0 Unit cell: (103.88, 101.76, 103.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 1476 8.00 N 1303 7.00 C 4967 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 70 " - pdb=" SG CYS B 258 " distance=2.81 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 130 " distance=2.50 Simple disulfide: pdb=" SG CYS B 193 " - pdb=" SG CYS B 227 " distance=2.87 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 239 " distance=2.21 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 1.0 seconds 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1828 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 55.3% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 83 through 100 Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 124 through 139 Processing helix chain 'A' and resid 142 through 156 Processing helix chain 'A' and resid 170 through 184 removed outlier: 3.612A pdb=" N ALA A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 206 through 225 removed outlier: 3.604A pdb=" N TYR A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 314 through 331 removed outlier: 4.074A pdb=" N ILE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 362 through 383 Processing helix chain 'A' and resid 390 through 407 Processing helix chain 'A' and resid 412 through 423 Processing helix chain 'A' and resid 429 through 442 removed outlier: 4.813A pdb=" N LYS A 442 " --> pdb=" O MET A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 461 Processing helix chain 'A' and resid 462 through 465 removed outlier: 3.907A pdb=" N LYS A 465 " --> pdb=" O PRO A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 465' Processing helix chain 'A' and resid 468 through 480 Processing helix chain 'A' and resid 481 through 494 removed outlier: 3.615A pdb=" N TYR A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 517 removed outlier: 4.190A pdb=" N GLU A 517 " --> pdb=" O VAL A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 removed outlier: 4.119A pdb=" N THR A 526 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 550 removed outlier: 3.539A pdb=" N LEU A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN A 549 " --> pdb=" O GLN A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 563 Processing helix chain 'A' and resid 576 through 594 removed outlier: 3.874A pdb=" N SER A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 594 " --> pdb=" O ALA A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 609 removed outlier: 4.113A pdb=" N GLY A 599 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 600 " --> pdb=" O ILE A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 624 removed outlier: 3.750A pdb=" N ALA A 617 " --> pdb=" O SER A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.516A pdb=" N HIS A 640 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 662 removed outlier: 3.714A pdb=" N ASP A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 684 Processing helix chain 'B' and resid 41 through 49 removed outlier: 3.637A pdb=" N ILE B 49 " --> pdb=" O TRP B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 58 removed outlier: 3.785A pdb=" N MET B 56 " --> pdb=" O ASN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 114 Processing helix chain 'B' and resid 236 through 245 removed outlier: 3.524A pdb=" N ASN B 240 " --> pdb=" O GLU B 237 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU B 242 " --> pdb=" O CYS B 239 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU B 243 " --> pdb=" O ASN B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 314 through 332 removed outlier: 3.688A pdb=" N TYR B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 62 removed outlier: 7.068A pdb=" N VAL A 61 " --> pdb=" O UNK A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 35 through 40 removed outlier: 6.193A pdb=" N LEU B 36 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N CYS B 258 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N SER B 38 " --> pdb=" O CYS B 258 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 122 removed outlier: 3.962A pdb=" N VAL B 136 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 173 through 176 removed outlier: 8.895A pdb=" N TYR B 181 " --> pdb=" O CYS B 208 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N CYS B 208 " --> pdb=" O TYR B 181 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR B 229 " --> pdb=" O MET B 201 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP B 220 " --> pdb=" O GLN B 232 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR B 234 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ILE B 218 " --> pdb=" O THR B 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 277 through 278 removed outlier: 3.528A pdb=" N ARG B 290 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR B 363 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN B 368 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLU B 376 " --> pdb=" O ASN B 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 277 through 278 removed outlier: 3.528A pdb=" N ARG B 290 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 347 " --> pdb=" O LYS B 396 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2453 1.34 - 1.46: 1438 1.46 - 1.58: 4006 1.58 - 1.70: 0 1.70 - 1.82: 63 Bond restraints: 7960 Sorted by residual: bond pdb=" C ARG B 116 " pdb=" N CYS B 117 " ideal model delta sigma weight residual 1.330 1.235 0.095 1.38e-02 5.25e+03 4.71e+01 bond pdb=" C CYS B 117 " pdb=" N ILE B 118 " ideal model delta sigma weight residual 1.333 1.248 0.085 1.34e-02 5.57e+03 4.04e+01 bond pdb=" CE1 HIS B 139 " pdb=" NE2 HIS B 139 " ideal model delta sigma weight residual 1.321 1.351 -0.030 1.00e-02 1.00e+04 9.25e+00 bond pdb=" N VAL B 179 " pdb=" CA VAL B 179 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.57e+00 bond pdb=" N TYR B 181 " pdb=" CA TYR B 181 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.31e-02 5.83e+03 8.52e+00 ... (remaining 7955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 10108 1.86 - 3.72: 557 3.72 - 5.58: 84 5.58 - 7.44: 21 7.44 - 9.30: 1 Bond angle restraints: 10771 Sorted by residual: angle pdb=" N LEU B 68 " pdb=" CA LEU B 68 " pdb=" C LEU B 68 " ideal model delta sigma weight residual 112.41 105.55 6.86 1.30e+00 5.92e-01 2.79e+01 angle pdb=" C LEU B 241 " pdb=" N GLU B 242 " pdb=" CA GLU B 242 " ideal model delta sigma weight residual 120.54 126.97 -6.43 1.35e+00 5.49e-01 2.27e+01 angle pdb=" CA ASN B 166 " pdb=" CB ASN B 166 " pdb=" CG ASN B 166 " ideal model delta sigma weight residual 112.60 117.34 -4.74 1.00e+00 1.00e+00 2.25e+01 angle pdb=" C CYS B 130 " pdb=" N PRO B 131 " pdb=" CA PRO B 131 " ideal model delta sigma weight residual 119.84 125.42 -5.58 1.25e+00 6.40e-01 1.99e+01 angle pdb=" N GLU B 242 " pdb=" CA GLU B 242 " pdb=" CB GLU B 242 " ideal model delta sigma weight residual 109.94 103.38 6.56 1.49e+00 4.50e-01 1.94e+01 ... (remaining 10766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 4189 16.84 - 33.68: 446 33.68 - 50.52: 98 50.52 - 67.36: 18 67.36 - 84.21: 14 Dihedral angle restraints: 4765 sinusoidal: 1921 harmonic: 2844 Sorted by residual: dihedral pdb=" CA ASN A 516 " pdb=" C ASN A 516 " pdb=" N GLU A 517 " pdb=" CA GLU A 517 " ideal model delta harmonic sigma weight residual 180.00 155.64 24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CB CYS B 208 " pdb=" SG CYS B 208 " pdb=" SG CYS B 239 " pdb=" CB CYS B 239 " ideal model delta sinusoidal sigma weight residual -86.00 -125.09 39.09 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CA ASN A 533 " pdb=" C ASN A 533 " pdb=" N ASP A 534 " pdb=" CA ASP A 534 " ideal model delta harmonic sigma weight residual 180.00 158.45 21.55 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 4762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 949 0.065 - 0.129: 165 0.129 - 0.194: 39 0.194 - 0.259: 5 0.259 - 0.324: 2 Chirality restraints: 1160 Sorted by residual: chirality pdb=" CB THR B 224 " pdb=" CA THR B 224 " pdb=" OG1 THR B 224 " pdb=" CG2 THR B 224 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA ARG B 116 " pdb=" N ARG B 116 " pdb=" C ARG B 116 " pdb=" CB ARG B 116 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB THR B 196 " pdb=" CA THR B 196 " pdb=" OG1 THR B 196 " pdb=" CG2 THR B 196 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1157 not shown) Planarity restraints: 1384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 125 " 0.209 2.00e-02 2.50e+03 1.05e-01 2.77e+02 pdb=" CG TRP B 125 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 125 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP B 125 " -0.112 2.00e-02 2.50e+03 pdb=" NE1 TRP B 125 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TRP B 125 " -0.022 2.00e-02 2.50e+03 pdb=" CE3 TRP B 125 " -0.135 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 125 " 0.119 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 125 " -0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP B 125 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 129 " 0.077 2.00e-02 2.50e+03 4.94e-02 4.88e+01 pdb=" CG TYR B 129 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR B 129 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR B 129 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR B 129 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 TYR B 129 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR B 129 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 129 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 110 " -0.048 2.00e-02 2.50e+03 3.06e-02 1.63e+01 pdb=" CG PHE B 110 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE B 110 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 110 " 0.036 2.00e-02 2.50e+03 pdb=" CE1 PHE B 110 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 110 " -0.022 2.00e-02 2.50e+03 pdb=" CZ PHE B 110 " -0.022 2.00e-02 2.50e+03 ... (remaining 1381 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 78 2.59 - 3.17: 6732 3.17 - 3.75: 11739 3.75 - 4.32: 15926 4.32 - 4.90: 26692 Nonbonded interactions: 61167 Sorted by model distance: nonbonded pdb=" O ASN B 309 " pdb=" OD1 ASN B 309 " model vdw 2.013 3.040 nonbonded pdb=" NE2 GLN B 250 " pdb=" ND2 ASN B 252 " model vdw 2.245 3.200 nonbonded pdb=" OG SER A 97 " pdb=" OG1 THR A 106 " model vdw 2.294 3.040 nonbonded pdb=" OD1 ASP A 231 " pdb=" NZ LYS A 456 " model vdw 2.305 3.120 nonbonded pdb=" CB PRO B 25 " pdb=" OH TYR B 176 " model vdw 2.307 3.440 ... (remaining 61162 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.540 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 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 0.095 7960 Z= 0.380 Angle : 0.934 9.296 10771 Z= 0.587 Chirality : 0.056 0.324 1160 Planarity : 0.007 0.105 1384 Dihedral : 14.845 84.206 2925 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.11 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % 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: -2.61 (0.24), residues: 940 helix: -0.92 (0.20), residues: 499 sheet: -1.96 (0.59), residues: 74 loop : -2.76 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.209 0.008 TRP B 125 HIS 0.008 0.001 HIS B 139 PHE 0.048 0.004 PHE B 110 TYR 0.086 0.002 TYR B 129 ARG 0.009 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 ASP cc_start: 0.8370 (m-30) cc_final: 0.8134 (m-30) REVERT: A 238 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8006 (mp0) REVERT: A 670 LYS cc_start: 0.6744 (mmtt) cc_final: 0.6488 (mmtt) REVERT: A 675 LYS cc_start: 0.8677 (tptm) cc_final: 0.7923 (tmmt) REVERT: B 64 MET cc_start: 0.8875 (mmt) cc_final: 0.8591 (mmt) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2400 time to fit residues: 44.4543 Evaluate side-chains 98 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN A 208 HIS B 121 GLN B 326 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7960 Z= 0.216 Angle : 0.556 6.784 10771 Z= 0.298 Chirality : 0.041 0.147 1160 Planarity : 0.003 0.043 1384 Dihedral : 4.466 22.237 1060 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.26 % Allowed : 14.03 % Favored : 83.71 % 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: -1.00 (0.26), residues: 940 helix: 0.53 (0.23), residues: 501 sheet: -1.76 (0.51), residues: 91 loop : -2.11 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 125 HIS 0.002 0.001 HIS A 638 PHE 0.014 0.001 PHE A 201 TYR 0.010 0.001 TYR B 182 ARG 0.003 0.000 ARG B 200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 136 ASP cc_start: 0.8294 (m-30) cc_final: 0.8070 (m-30) REVERT: A 184 LEU cc_start: 0.9396 (mt) cc_final: 0.9068 (mt) REVERT: A 347 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8485 (mm) REVERT: A 639 GLU cc_start: 0.8770 (pp20) cc_final: 0.8107 (pt0) REVERT: A 670 LYS cc_start: 0.6982 (mmtt) cc_final: 0.6519 (mmtt) REVERT: A 675 LYS cc_start: 0.8588 (tptm) cc_final: 0.7856 (ttpt) REVERT: B 39 TYR cc_start: 0.8168 (m-80) cc_final: 0.7948 (m-10) REVERT: B 64 MET cc_start: 0.8970 (mmt) cc_final: 0.8744 (mmp) REVERT: B 278 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8265 (tm-30) outliers start: 19 outliers final: 9 residues processed: 139 average time/residue: 0.1857 time to fit residues: 35.8950 Evaluate side-chains 115 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 380 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 72 optimal weight: 0.0870 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 87 optimal weight: 0.0980 chunk 94 optimal weight: 0.0770 chunk 77 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7960 Z= 0.147 Angle : 0.502 9.531 10771 Z= 0.264 Chirality : 0.038 0.136 1160 Planarity : 0.003 0.040 1384 Dihedral : 4.200 21.296 1060 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.97 % Allowed : 16.05 % Favored : 80.98 % 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: -0.35 (0.27), residues: 940 helix: 1.12 (0.23), residues: 500 sheet: -1.36 (0.58), residues: 79 loop : -1.93 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 541 HIS 0.002 0.001 HIS A 638 PHE 0.011 0.001 PHE A 367 TYR 0.009 0.001 TYR A 368 ARG 0.002 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 ASP cc_start: 0.8307 (m-30) cc_final: 0.8075 (m-30) REVERT: A 183 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7884 (mm-40) REVERT: A 347 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8464 (mm) REVERT: A 390 ASN cc_start: 0.8756 (m-40) cc_final: 0.8541 (t0) REVERT: A 639 GLU cc_start: 0.8692 (pp20) cc_final: 0.8181 (tt0) REVERT: A 670 LYS cc_start: 0.6837 (mmtt) cc_final: 0.6374 (mmtt) REVERT: B 64 MET cc_start: 0.8965 (mmt) cc_final: 0.8713 (mmp) REVERT: B 134 GLU cc_start: 0.1523 (OUTLIER) cc_final: 0.1214 (pp20) REVERT: B 175 LEU cc_start: 0.6084 (OUTLIER) cc_final: 0.5878 (mp) outliers start: 25 outliers final: 13 residues processed: 140 average time/residue: 0.1712 time to fit residues: 34.1676 Evaluate side-chains 126 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 380 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 45 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 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 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7960 Z= 0.166 Angle : 0.497 7.863 10771 Z= 0.262 Chirality : 0.039 0.130 1160 Planarity : 0.003 0.042 1384 Dihedral : 4.019 20.650 1060 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.57 % Allowed : 17.48 % Favored : 78.95 % 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: -0.05 (0.28), residues: 940 helix: 1.36 (0.23), residues: 505 sheet: -1.27 (0.60), residues: 79 loop : -1.82 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 45 HIS 0.003 0.000 HIS A 122 PHE 0.010 0.001 PHE A 452 TYR 0.009 0.001 TYR A 368 ARG 0.003 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 115 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7898 (mm-40) REVERT: A 347 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8589 (mm) REVERT: A 380 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.7928 (m-10) REVERT: A 428 ASN cc_start: 0.7712 (m110) cc_final: 0.6597 (t0) REVERT: A 444 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7715 (tp40) REVERT: A 642 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7073 (pp) REVERT: B 64 MET cc_start: 0.8869 (mmt) cc_final: 0.8588 (mmp) REVERT: B 175 LEU cc_start: 0.6159 (OUTLIER) cc_final: 0.5916 (mp) REVERT: B 216 SER cc_start: 0.1615 (OUTLIER) cc_final: 0.0606 (t) REVERT: B 278 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8240 (tm-30) outliers start: 30 outliers final: 13 residues processed: 135 average time/residue: 0.1862 time to fit residues: 35.7271 Evaluate side-chains 126 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 380 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 83 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 7960 Z= 0.458 Angle : 0.661 7.478 10771 Z= 0.347 Chirality : 0.045 0.147 1160 Planarity : 0.004 0.046 1384 Dihedral : 4.750 23.874 1060 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.76 % Allowed : 18.91 % Favored : 76.34 % 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: -0.39 (0.27), residues: 940 helix: 1.01 (0.23), residues: 504 sheet: -1.43 (0.58), residues: 79 loop : -1.84 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 45 HIS 0.004 0.001 HIS A 143 PHE 0.012 0.002 PHE A 481 TYR 0.015 0.002 TYR B 127 ARG 0.004 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 107 time to evaluate : 0.770 Fit side-chains REVERT: A 380 TYR cc_start: 0.8983 (OUTLIER) cc_final: 0.7966 (m-10) REVERT: A 666 TYR cc_start: 0.8459 (t80) cc_final: 0.8229 (t80) REVERT: A 670 LYS cc_start: 0.7088 (mmtt) cc_final: 0.6648 (mptt) REVERT: B 64 MET cc_start: 0.8969 (mmt) cc_final: 0.8693 (mmp) REVERT: B 216 SER cc_start: 0.2874 (OUTLIER) cc_final: 0.1917 (t) REVERT: B 278 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8284 (tm-30) outliers start: 40 outliers final: 22 residues processed: 137 average time/residue: 0.1744 time to fit residues: 33.5752 Evaluate side-chains 125 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 380 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 22 optimal weight: 0.0670 chunk 92 optimal weight: 0.3980 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7960 Z= 0.157 Angle : 0.523 10.008 10771 Z= 0.274 Chirality : 0.039 0.147 1160 Planarity : 0.003 0.039 1384 Dihedral : 4.258 20.285 1060 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.21 % Allowed : 21.17 % Favored : 75.62 % 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: 0.05 (0.27), residues: 940 helix: 1.43 (0.23), residues: 503 sheet: -1.18 (0.59), residues: 79 loop : -1.75 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 45 HIS 0.003 0.001 HIS A 122 PHE 0.008 0.001 PHE B 288 TYR 0.010 0.001 TYR A 619 ARG 0.003 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: A 60 TYR cc_start: 0.7878 (m-80) cc_final: 0.7660 (m-80) REVERT: A 152 MET cc_start: 0.8883 (ttm) cc_final: 0.8531 (ttp) REVERT: A 183 GLN cc_start: 0.8140 (mt0) cc_final: 0.7802 (mm-40) REVERT: A 347 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8362 (mm) REVERT: A 348 GLU cc_start: 0.7443 (tp30) cc_final: 0.7080 (tp30) REVERT: A 380 TYR cc_start: 0.8793 (OUTLIER) cc_final: 0.7863 (m-10) REVERT: A 444 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7767 (tp40) REVERT: A 639 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: A 670 LYS cc_start: 0.6819 (mmtt) cc_final: 0.6384 (mmtt) REVERT: B 64 MET cc_start: 0.8959 (mmt) cc_final: 0.8724 (mmp) REVERT: B 136 VAL cc_start: 0.0637 (OUTLIER) cc_final: 0.0332 (t) REVERT: B 216 SER cc_start: 0.2736 (OUTLIER) cc_final: 0.1787 (t) REVERT: B 278 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8289 (tm-30) outliers start: 27 outliers final: 16 residues processed: 132 average time/residue: 0.1863 time to fit residues: 35.0460 Evaluate side-chains 127 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 380 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7960 Z= 0.214 Angle : 0.549 9.377 10771 Z= 0.283 Chirality : 0.040 0.171 1160 Planarity : 0.003 0.052 1384 Dihedral : 4.187 21.065 1060 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.57 % Allowed : 21.05 % Favored : 75.39 % 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: 0.15 (0.28), residues: 940 helix: 1.48 (0.23), residues: 506 sheet: -1.13 (0.59), residues: 79 loop : -1.67 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 45 HIS 0.003 0.001 HIS A 143 PHE 0.010 0.001 PHE A 452 TYR 0.013 0.001 TYR A 74 ARG 0.003 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 113 time to evaluate : 0.843 Fit side-chains REVERT: A 60 TYR cc_start: 0.7897 (m-80) cc_final: 0.7647 (m-80) REVERT: A 152 MET cc_start: 0.8902 (ttm) cc_final: 0.8543 (mtp) REVERT: A 347 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8473 (mm) REVERT: A 348 GLU cc_start: 0.7530 (tp30) cc_final: 0.7187 (tp30) REVERT: A 380 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.7776 (m-10) REVERT: A 444 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7832 (tp40) REVERT: A 478 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9276 (mm) REVERT: A 639 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8311 (tt0) REVERT: A 670 LYS cc_start: 0.6886 (mmtt) cc_final: 0.6420 (mmtt) REVERT: B 64 MET cc_start: 0.9004 (mmt) cc_final: 0.8757 (mmp) REVERT: B 136 VAL cc_start: 0.0554 (OUTLIER) cc_final: 0.0277 (t) REVERT: B 216 SER cc_start: 0.2624 (OUTLIER) cc_final: 0.1666 (t) outliers start: 30 outliers final: 21 residues processed: 136 average time/residue: 0.1702 time to fit residues: 32.9445 Evaluate side-chains 133 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 106 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 380 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 0.0870 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 63 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 72 optimal weight: 0.0970 chunk 84 optimal weight: 0.8980 chunk 88 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7960 Z= 0.146 Angle : 0.524 9.119 10771 Z= 0.269 Chirality : 0.038 0.152 1160 Planarity : 0.003 0.046 1384 Dihedral : 3.993 19.057 1060 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.33 % Allowed : 22.00 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.28), residues: 940 helix: 1.61 (0.23), residues: 505 sheet: -0.95 (0.59), residues: 79 loop : -1.60 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 45 HIS 0.003 0.001 HIS A 122 PHE 0.008 0.001 PHE B 110 TYR 0.010 0.001 TYR A 619 ARG 0.003 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 115 time to evaluate : 0.837 Fit side-chains REVERT: A 60 TYR cc_start: 0.7778 (m-80) cc_final: 0.7572 (m-80) REVERT: A 136 ASP cc_start: 0.8343 (m-30) cc_final: 0.8132 (m-30) REVERT: A 152 MET cc_start: 0.8829 (ttm) cc_final: 0.8440 (mtp) REVERT: A 348 GLU cc_start: 0.7469 (tp30) cc_final: 0.7121 (tp30) REVERT: A 380 TYR cc_start: 0.8682 (OUTLIER) cc_final: 0.7830 (m-10) REVERT: A 428 ASN cc_start: 0.7357 (m-40) cc_final: 0.6704 (t0) REVERT: A 444 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7757 (tp40) REVERT: A 478 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9253 (mm) REVERT: A 639 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: A 670 LYS cc_start: 0.6883 (mmtt) cc_final: 0.6461 (mptt) REVERT: B 64 MET cc_start: 0.8912 (mmt) cc_final: 0.8644 (mmp) REVERT: B 203 GLU cc_start: 0.2870 (OUTLIER) cc_final: 0.2667 (tm-30) REVERT: B 216 SER cc_start: 0.2771 (OUTLIER) cc_final: 0.1838 (t) outliers start: 28 outliers final: 17 residues processed: 136 average time/residue: 0.1678 time to fit residues: 32.4405 Evaluate side-chains 126 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 380 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.766 > 50: distance: 59 - 64: 5.734 distance: 64 - 65: 8.013 distance: 65 - 66: 23.712 distance: 65 - 68: 9.162 distance: 66 - 67: 19.441 distance: 66 - 72: 8.640 distance: 68 - 69: 21.588 distance: 68 - 70: 11.542 distance: 69 - 71: 18.147 distance: 72 - 73: 10.111 distance: 73 - 74: 26.787 distance: 73 - 76: 10.578 distance: 74 - 75: 32.431 distance: 74 - 83: 18.959 distance: 76 - 77: 4.987 distance: 77 - 78: 3.062 distance: 77 - 79: 20.431 distance: 78 - 80: 5.696 distance: 79 - 81: 11.046 distance: 80 - 82: 20.470 distance: 81 - 82: 11.552 distance: 83 - 84: 11.643 distance: 84 - 85: 16.172 distance: 84 - 87: 4.036 distance: 85 - 86: 16.109 distance: 85 - 91: 10.521 distance: 87 - 88: 15.352 distance: 88 - 89: 12.214 distance: 88 - 90: 14.094 distance: 91 - 92: 8.753 distance: 92 - 93: 19.709 distance: 93 - 94: 23.929 distance: 93 - 95: 6.984 distance: 95 - 96: 8.696 distance: 96 - 97: 32.784 distance: 96 - 99: 26.089 distance: 97 - 98: 22.357 distance: 97 - 101: 17.751 distance: 99 - 100: 30.571 distance: 101 - 102: 12.086 distance: 102 - 103: 15.870 distance: 103 - 104: 5.219 distance: 103 - 105: 29.044 distance: 105 - 106: 22.149 distance: 106 - 107: 8.411 distance: 106 - 109: 26.147 distance: 107 - 108: 7.997 distance: 109 - 110: 26.223 distance: 109 - 111: 18.017 distance: 110 - 112: 13.251 distance: 113 - 114: 12.083 distance: 113 - 183: 17.858 distance: 114 - 115: 4.749 distance: 114 - 117: 3.654 distance: 115 - 125: 19.751 distance: 116 - 180: 20.781 distance: 117 - 118: 4.363 distance: 118 - 119: 8.740 distance: 118 - 120: 10.752 distance: 119 - 121: 8.247 distance: 120 - 122: 4.030 distance: 121 - 123: 9.485 distance: 122 - 123: 9.856 distance: 123 - 124: 21.490 distance: 125 - 126: 14.753 distance: 126 - 127: 13.643 distance: 126 - 129: 8.326 distance: 127 - 128: 18.113 distance: 127 - 136: 10.086 distance: 129 - 130: 17.668 distance: 130 - 131: 25.106 distance: 130 - 132: 14.992 distance: 131 - 133: 18.738 distance: 132 - 134: 9.385 distance: 133 - 135: 20.651 distance: 134 - 135: 8.747 distance: 136 - 137: 11.725 distance: 136 - 168: 21.025 distance: 137 - 138: 18.858 distance: 137 - 140: 28.930 distance: 138 - 139: 3.501 distance: 138 - 144: 22.283 distance: 139 - 165: 18.769 distance: 140 - 141: 7.853 distance: 141 - 142: 9.825 distance: 141 - 143: 5.644