Starting phenix.real_space_refine on Sat Jan 18 18:15:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ze0_60019/01_2025/8ze0_60019.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ze0_60019/01_2025/8ze0_60019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ze0_60019/01_2025/8ze0_60019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ze0_60019/01_2025/8ze0_60019.map" model { file = "/net/cci-nas-00/data/ceres_data/8ze0_60019/01_2025/8ze0_60019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ze0_60019/01_2025/8ze0_60019.cif" } resolution = 2.54 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= 0.007 sd= 0.050 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 92 5.16 5 C 8528 2.51 5 N 2124 2.21 5 O 2136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 12880 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3220 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 377} Restraints were copied for chains: C, B, D Time building chain proxies: 6.51, per 1000 atoms: 0.51 Number of scatterers: 12880 At special positions: 0 Unit cell: (116.5, 116.5, 98.792, 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 92 16.00 O 2136 8.00 N 2124 7.00 C 8528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 3.33 Conformation dependent library (CDL) restraints added in 1.6 seconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 78.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 58 through 73 Proline residue: A 65 - end of helix removed outlier: 3.594A pdb=" N LEU A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 123 Processing helix chain 'A' and resid 128 through 164 removed outlier: 4.364A pdb=" N LEU A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 177 through 214 removed outlier: 3.591A pdb=" N MET A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 231 Processing helix chain 'A' and resid 242 through 287 removed outlier: 4.096A pdb=" N ASP A 264 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 341 removed outlier: 3.559A pdb=" N PHE A 298 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 387 removed outlier: 3.978A pdb=" N ILE A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'A' and resid 421 through 444 removed outlier: 4.127A pdb=" N GLN A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE A 442 " --> pdb=" O VAL A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'B' and resid 58 through 73 Proline residue: B 65 - end of helix removed outlier: 3.595A pdb=" N LEU B 69 " --> pdb=" O PRO B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 123 Processing helix chain 'B' and resid 128 through 164 removed outlier: 4.363A pdb=" N LEU B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 177 through 214 removed outlier: 3.592A pdb=" N MET B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 242 through 287 removed outlier: 4.097A pdb=" N ASP B 264 " --> pdb=" O TRP B 260 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 341 removed outlier: 3.559A pdb=" N PHE B 298 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER B 321 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 387 removed outlier: 3.977A pdb=" N ILE B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASN B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B 385 " --> pdb=" O ARG B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 408 Processing helix chain 'B' and resid 421 through 444 removed outlier: 4.126A pdb=" N GLN B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE B 442 " --> pdb=" O VAL B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'C' and resid 58 through 73 Proline residue: C 65 - end of helix removed outlier: 3.595A pdb=" N LEU C 69 " --> pdb=" O PRO C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 123 Processing helix chain 'C' and resid 128 through 164 removed outlier: 4.364A pdb=" N LEU C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Proline residue: C 153 - end of helix Processing helix chain 'C' and resid 165 through 168 Processing helix chain 'C' and resid 177 through 214 removed outlier: 3.591A pdb=" N MET C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 242 through 287 removed outlier: 4.097A pdb=" N ASP C 264 " --> pdb=" O TRP C 260 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG C 277 " --> pdb=" O GLY C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 341 removed outlier: 3.559A pdb=" N PHE C 298 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 387 removed outlier: 3.978A pdb=" N ILE C 375 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASN C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL C 385 " --> pdb=" O ARG C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 408 Processing helix chain 'C' and resid 421 through 444 removed outlier: 4.126A pdb=" N GLN C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE C 442 " --> pdb=" O VAL C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 447 No H-bonds generated for 'chain 'C' and resid 445 through 447' Processing helix chain 'D' and resid 58 through 73 Proline residue: D 65 - end of helix removed outlier: 3.594A pdb=" N LEU D 69 " --> pdb=" O PRO D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 123 Processing helix chain 'D' and resid 128 through 164 removed outlier: 4.364A pdb=" N LEU D 132 " --> pdb=" O ASN D 128 " (cutoff:3.500A) Proline residue: D 153 - end of helix Processing helix chain 'D' and resid 165 through 168 Processing helix chain 'D' and resid 177 through 214 removed outlier: 3.590A pdb=" N MET D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 231 Processing helix chain 'D' and resid 242 through 287 removed outlier: 4.097A pdb=" N ASP D 264 " --> pdb=" O TRP D 260 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 341 removed outlier: 3.559A pdb=" N PHE D 298 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 387 removed outlier: 3.978A pdb=" N ILE D 375 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASN D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU D 383 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL D 385 " --> pdb=" O ARG D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'D' and resid 421 through 444 removed outlier: 4.127A pdb=" N GLN D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE D 442 " --> pdb=" O VAL D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 447 No H-bonds generated for 'chain 'D' and resid 445 through 447' 964 hydrogen bonds defined for protein. 2880 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: 3.47 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3912 1.34 - 1.46: 3209 1.46 - 1.58: 5935 1.58 - 1.70: 0 1.70 - 1.81: 148 Bond restraints: 13204 Sorted by residual: bond pdb=" CA TYR B 234 " pdb=" CB TYR B 234 " ideal model delta sigma weight residual 1.530 1.548 -0.017 1.69e-02 3.50e+03 1.07e+00 bond pdb=" CA TYR A 234 " pdb=" CB TYR A 234 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 9.89e-01 bond pdb=" CA TYR C 234 " pdb=" CB TYR C 234 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 9.83e-01 bond pdb=" CA TYR D 234 " pdb=" CB TYR D 234 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 9.27e-01 bond pdb=" CA VAL D 410 " pdb=" CB VAL D 410 " ideal model delta sigma weight residual 1.531 1.541 -0.010 1.11e-02 8.12e+03 7.82e-01 ... (remaining 13199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 17553 1.60 - 3.20: 274 3.20 - 4.80: 54 4.80 - 6.40: 11 6.40 - 8.00: 16 Bond angle restraints: 17908 Sorted by residual: angle pdb=" C ASP B 233 " pdb=" N TYR B 234 " pdb=" CA TYR B 234 " ideal model delta sigma weight residual 121.54 128.06 -6.52 1.91e+00 2.74e-01 1.16e+01 angle pdb=" C ASP D 233 " pdb=" N TYR D 234 " pdb=" CA TYR D 234 " ideal model delta sigma weight residual 121.54 128.00 -6.46 1.91e+00 2.74e-01 1.14e+01 angle pdb=" C ASP C 233 " pdb=" N TYR C 234 " pdb=" CA TYR C 234 " ideal model delta sigma weight residual 121.54 127.98 -6.44 1.91e+00 2.74e-01 1.14e+01 angle pdb=" C ASP A 233 " pdb=" N TYR A 234 " pdb=" CA TYR A 234 " ideal model delta sigma weight residual 121.54 127.95 -6.41 1.91e+00 2.74e-01 1.12e+01 angle pdb=" N TRP B 152 " pdb=" CA TRP B 152 " pdb=" C TRP B 152 " ideal model delta sigma weight residual 109.81 115.22 -5.41 2.21e+00 2.05e-01 6.00e+00 ... (remaining 17903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 6581 16.88 - 33.76: 895 33.76 - 50.63: 284 50.63 - 67.51: 48 67.51 - 84.39: 16 Dihedral angle restraints: 7824 sinusoidal: 3156 harmonic: 4668 Sorted by residual: dihedral pdb=" CG ARG A 364 " pdb=" CD ARG A 364 " pdb=" NE ARG A 364 " pdb=" CZ ARG A 364 " ideal model delta sinusoidal sigma weight residual -180.00 -137.14 -42.86 2 1.50e+01 4.44e-03 9.87e+00 dihedral pdb=" CG ARG D 364 " pdb=" CD ARG D 364 " pdb=" NE ARG D 364 " pdb=" CZ ARG D 364 " ideal model delta sinusoidal sigma weight residual -180.00 -137.15 -42.85 2 1.50e+01 4.44e-03 9.87e+00 dihedral pdb=" CG ARG B 364 " pdb=" CD ARG B 364 " pdb=" NE ARG B 364 " pdb=" CZ ARG B 364 " ideal model delta sinusoidal sigma weight residual -180.00 -137.15 -42.85 2 1.50e+01 4.44e-03 9.87e+00 ... (remaining 7821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1288 0.028 - 0.056: 501 0.056 - 0.084: 195 0.084 - 0.113: 68 0.113 - 0.141: 16 Chirality restraints: 2068 Sorted by residual: chirality pdb=" CA TYR A 234 " pdb=" N TYR A 234 " pdb=" C TYR A 234 " pdb=" CB TYR A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA TYR D 234 " pdb=" N TYR D 234 " pdb=" C TYR D 234 " pdb=" CB TYR D 234 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA TYR C 234 " pdb=" N TYR C 234 " pdb=" C TYR C 234 " pdb=" CB TYR C 234 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 2065 not shown) Planarity restraints: 2184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP D 152 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO D 153 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 153 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 153 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 152 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO A 153 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 152 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO B 153 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 153 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 153 " -0.030 5.00e-02 4.00e+02 ... (remaining 2181 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2976 2.78 - 3.31: 12547 3.31 - 3.84: 22524 3.84 - 4.37: 25245 4.37 - 4.90: 43694 Nonbonded interactions: 106986 Sorted by model distance: nonbonded pdb=" OD2 ASP A 316 " pdb=" OG SER A 413 " model vdw 2.254 3.040 nonbonded pdb=" OD2 ASP D 316 " pdb=" OG SER D 413 " model vdw 2.254 3.040 nonbonded pdb=" OD2 ASP C 316 " pdb=" OG SER C 413 " model vdw 2.254 3.040 nonbonded pdb=" OD2 ASP B 316 " pdb=" OG SER B 413 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASN B 225 " pdb=" OH TYR B 241 " model vdw 2.317 3.040 ... (remaining 106981 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 28.170 Find NCS groups from input model: 0.220 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:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 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 : 0.002 0.027 13204 Z= 0.149 Angle : 0.553 8.005 17908 Z= 0.292 Chirality : 0.037 0.141 2068 Planarity : 0.004 0.054 2184 Dihedral : 17.024 84.391 4800 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.31 % Favored : 97.44 % Rotamer: Outliers : 0.28 % Allowed : 22.82 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.35 (0.20), residues: 1560 helix: 2.41 (0.14), residues: 1168 sheet: None (None), residues: 0 loop : -1.18 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 394 HIS 0.001 0.000 HIS B 290 PHE 0.020 0.001 PHE D 354 TYR 0.013 0.001 TYR B 227 ARG 0.003 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 394 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 394 average time/residue: 0.8292 time to fit residues: 369.3317 Evaluate side-chains 260 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 231 ASN B 71 GLN B 231 ASN C 71 GLN C 231 ASN D 71 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.082596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.064929 restraints weight = 31741.280| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.71 r_work: 0.2893 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13204 Z= 0.229 Angle : 0.631 9.512 17908 Z= 0.317 Chirality : 0.041 0.142 2068 Planarity : 0.005 0.052 2184 Dihedral : 3.611 11.841 1754 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.92 % Favored : 97.82 % Rotamer: Outliers : 4.08 % Allowed : 24.93 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.32 (0.20), residues: 1560 helix: 2.29 (0.14), residues: 1176 sheet: None (None), residues: 0 loop : -0.91 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 347 HIS 0.005 0.001 HIS D 118 PHE 0.024 0.001 PHE D 224 TYR 0.015 0.002 TYR B 262 ARG 0.007 0.000 ARG C 392 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 274 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 LEU cc_start: 0.9425 (tp) cc_final: 0.9201 (tm) REVERT: A 196 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8939 (tp30) REVERT: B 106 ILE cc_start: 0.9603 (OUTLIER) cc_final: 0.9372 (mp) REVERT: B 109 SER cc_start: 0.9124 (p) cc_final: 0.8782 (p) REVERT: C 71 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8637 (tp40) REVERT: C 253 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8448 (t0) outliers start: 58 outliers final: 18 residues processed: 312 average time/residue: 0.7606 time to fit residues: 273.2407 Evaluate side-chains 271 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 250 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 317 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 123 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 89 optimal weight: 0.0170 chunk 95 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN B 71 GLN B 253 ASN D 71 GLN D 253 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.080812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.063119 restraints weight = 32324.604| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.69 r_work: 0.2853 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13204 Z= 0.269 Angle : 0.623 10.189 17908 Z= 0.313 Chirality : 0.041 0.236 2068 Planarity : 0.004 0.046 2184 Dihedral : 3.569 16.125 1752 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.99 % Favored : 97.76 % Rotamer: Outliers : 4.37 % Allowed : 24.51 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.51 (0.20), residues: 1560 helix: 2.44 (0.14), residues: 1176 sheet: None (None), residues: 0 loop : -0.86 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 347 HIS 0.003 0.001 HIS D 118 PHE 0.016 0.001 PHE A 224 TYR 0.014 0.001 TYR D 208 ARG 0.005 0.000 ARG D 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 250 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ILE cc_start: 0.9585 (mp) cc_final: 0.9336 (mp) REVERT: A 313 GLU cc_start: 0.9135 (tp30) cc_final: 0.8933 (tp30) REVERT: A 428 MET cc_start: 0.9543 (ttt) cc_final: 0.9087 (ttt) REVERT: B 71 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8606 (tp40) REVERT: C 98 MET cc_start: 0.9424 (tpt) cc_final: 0.9188 (tpt) REVERT: D 206 LEU cc_start: 0.9574 (tp) cc_final: 0.9343 (tp) REVERT: D 440 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9164 (mm) outliers start: 62 outliers final: 19 residues processed: 297 average time/residue: 0.7224 time to fit residues: 247.6980 Evaluate side-chains 253 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 64 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN C 71 GLN D 71 GLN D 253 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.081461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.063545 restraints weight = 31388.878| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.69 r_work: 0.2865 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13204 Z= 0.187 Angle : 0.593 11.002 17908 Z= 0.296 Chirality : 0.040 0.304 2068 Planarity : 0.004 0.042 2184 Dihedral : 3.520 12.508 1752 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.05 % Favored : 97.69 % Rotamer: Outliers : 3.45 % Allowed : 24.23 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.55 (0.20), residues: 1560 helix: 2.47 (0.14), residues: 1176 sheet: None (None), residues: 0 loop : -0.90 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 347 HIS 0.003 0.001 HIS A 118 PHE 0.015 0.001 PHE D 64 TYR 0.016 0.001 TYR D 208 ARG 0.002 0.000 ARG D 423 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 249 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ILE cc_start: 0.9566 (mp) cc_final: 0.9340 (mp) REVERT: A 113 LEU cc_start: 0.9583 (tm) cc_final: 0.9383 (mm) REVERT: A 381 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8181 (mtt90) REVERT: B 184 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9278 (mm) REVERT: D 98 MET cc_start: 0.9425 (tpt) cc_final: 0.9174 (tpt) REVERT: D 440 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8992 (mm) REVERT: D 441 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8459 (mm-40) outliers start: 49 outliers final: 22 residues processed: 282 average time/residue: 0.8005 time to fit residues: 257.9559 Evaluate side-chains 258 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 233 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 53 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 121 optimal weight: 0.0020 chunk 72 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 33 optimal weight: 0.0470 chunk 62 optimal weight: 0.7980 overall best weight: 0.5688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN C 71 GLN C 253 ASN D 71 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.082253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.064202 restraints weight = 31428.654| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.77 r_work: 0.2881 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13204 Z= 0.165 Angle : 0.595 12.434 17908 Z= 0.294 Chirality : 0.039 0.303 2068 Planarity : 0.004 0.040 2184 Dihedral : 3.483 12.638 1752 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.99 % Favored : 97.76 % Rotamer: Outliers : 3.59 % Allowed : 24.86 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.62 (0.20), residues: 1560 helix: 2.52 (0.14), residues: 1176 sheet: None (None), residues: 0 loop : -0.88 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 347 HIS 0.003 0.001 HIS A 118 PHE 0.015 0.001 PHE B 224 TYR 0.018 0.001 TYR D 208 ARG 0.005 0.000 ARG D 423 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 252 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ILE cc_start: 0.9562 (mp) cc_final: 0.9349 (mp) REVERT: A 381 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8193 (mtt90) REVERT: B 184 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9264 (mm) REVERT: C 76 MET cc_start: 0.8432 (mtp) cc_final: 0.8183 (ttt) REVERT: C 98 MET cc_start: 0.9419 (tpt) cc_final: 0.9202 (tpt) REVERT: D 98 MET cc_start: 0.9373 (tpt) cc_final: 0.9102 (tpt) REVERT: D 432 ILE cc_start: 0.9546 (mt) cc_final: 0.9279 (mp) REVERT: D 440 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8958 (mm) REVERT: D 441 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8291 (mm110) outliers start: 51 outliers final: 28 residues processed: 284 average time/residue: 0.7616 time to fit residues: 249.1967 Evaluate side-chains 266 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 367 PHE Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain D residue 367 PHE Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 137 optimal weight: 0.6980 chunk 150 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN B 71 GLN D 71 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.081244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.063312 restraints weight = 31965.802| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.77 r_work: 0.2860 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13204 Z= 0.201 Angle : 0.612 12.687 17908 Z= 0.302 Chirality : 0.040 0.307 2068 Planarity : 0.004 0.041 2184 Dihedral : 3.451 12.624 1752 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.18 % Favored : 97.56 % Rotamer: Outliers : 4.08 % Allowed : 24.37 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.73 (0.21), residues: 1560 helix: 2.61 (0.14), residues: 1176 sheet: None (None), residues: 0 loop : -0.83 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 347 HIS 0.003 0.001 HIS A 118 PHE 0.015 0.001 PHE D 64 TYR 0.017 0.001 TYR D 208 ARG 0.004 0.000 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 243 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LEU cc_start: 0.9685 (tm) cc_final: 0.9443 (tm) REVERT: A 381 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8160 (mtt90) REVERT: B 184 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9288 (mm) REVERT: B 428 MET cc_start: 0.9643 (ttt) cc_final: 0.9290 (ttt) REVERT: C 76 MET cc_start: 0.8502 (mtp) cc_final: 0.8271 (ttt) REVERT: C 442 PHE cc_start: 0.8068 (m-80) cc_final: 0.7303 (m-80) REVERT: D 76 MET cc_start: 0.8519 (mtp) cc_final: 0.8190 (ttt) REVERT: D 432 ILE cc_start: 0.9578 (mt) cc_final: 0.9311 (mp) REVERT: D 440 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8987 (mm) REVERT: D 441 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8176 (mm110) outliers start: 58 outliers final: 28 residues processed: 282 average time/residue: 0.7613 time to fit residues: 246.5601 Evaluate side-chains 263 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 146 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 118 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN B 71 GLN C 71 GLN D 71 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.078898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.061741 restraints weight = 33110.257| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.70 r_work: 0.2833 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13204 Z= 0.259 Angle : 0.667 13.736 17908 Z= 0.326 Chirality : 0.042 0.242 2068 Planarity : 0.004 0.042 2184 Dihedral : 3.545 13.182 1752 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.24 % Favored : 97.50 % Rotamer: Outliers : 4.30 % Allowed : 25.14 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.79 (0.21), residues: 1560 helix: 2.64 (0.14), residues: 1176 sheet: None (None), residues: 0 loop : -0.78 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 347 HIS 0.004 0.001 HIS A 118 PHE 0.017 0.001 PHE A 64 TYR 0.020 0.002 TYR C 227 ARG 0.011 0.000 ARG C 423 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 246 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 ILE cc_start: 0.8800 (tt) cc_final: 0.8530 (tp) REVERT: A 428 MET cc_start: 0.9656 (ttt) cc_final: 0.9273 (ttt) REVERT: B 184 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9277 (mm) REVERT: B 428 MET cc_start: 0.9658 (ttt) cc_final: 0.9369 (ttt) REVERT: C 442 PHE cc_start: 0.8065 (m-80) cc_final: 0.7395 (m-80) REVERT: D 392 ARG cc_start: 0.8534 (ppt170) cc_final: 0.8324 (ppt170) REVERT: D 428 MET cc_start: 0.9661 (ttt) cc_final: 0.9275 (ttt) REVERT: D 440 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9106 (mm) REVERT: D 441 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8192 (mm-40) outliers start: 61 outliers final: 25 residues processed: 283 average time/residue: 0.7734 time to fit residues: 250.6221 Evaluate side-chains 253 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 226 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.032 > 50: distance: 8 - 31: 6.848 distance: 16 - 39: 10.265 distance: 20 - 44: 12.516 distance: 23 - 24: 3.388 distance: 24 - 25: 9.307 distance: 24 - 27: 5.506 distance: 25 - 26: 6.070 distance: 25 - 31: 11.016 distance: 26 - 51: 17.644 distance: 27 - 28: 6.532 distance: 28 - 29: 8.953 distance: 29 - 30: 11.875 distance: 31 - 32: 10.640 distance: 32 - 33: 8.911 distance: 32 - 35: 6.025 distance: 33 - 34: 7.144 distance: 33 - 39: 5.852 distance: 34 - 57: 22.325 distance: 35 - 36: 8.838 distance: 35 - 37: 4.108 distance: 36 - 38: 13.100 distance: 39 - 40: 9.511 distance: 40 - 41: 6.719 distance: 41 - 42: 7.735 distance: 41 - 44: 8.573 distance: 42 - 65: 21.574 distance: 44 - 45: 9.644 distance: 45 - 46: 3.566 distance: 45 - 48: 8.493 distance: 46 - 47: 9.296 distance: 46 - 51: 7.463 distance: 47 - 73: 14.029 distance: 48 - 49: 4.923 distance: 48 - 50: 3.946 distance: 51 - 52: 8.461 distance: 52 - 53: 5.206 distance: 52 - 55: 6.579 distance: 53 - 54: 17.006 distance: 53 - 57: 19.933 distance: 54 - 84: 15.598 distance: 55 - 56: 13.406 distance: 57 - 58: 24.827 distance: 58 - 59: 13.462 distance: 58 - 61: 29.532 distance: 59 - 60: 10.421 distance: 59 - 65: 14.489 distance: 60 - 92: 15.327 distance: 61 - 62: 19.478 distance: 61 - 63: 24.749 distance: 62 - 64: 3.909 distance: 65 - 66: 4.988 distance: 66 - 67: 11.038 distance: 66 - 69: 10.171 distance: 67 - 68: 8.539 distance: 67 - 73: 11.463 distance: 68 - 98: 3.343 distance: 69 - 70: 10.963 distance: 70 - 71: 17.731 distance: 70 - 72: 22.152 distance: 73 - 74: 7.711 distance: 74 - 75: 5.863 distance: 74 - 77: 4.256 distance: 75 - 76: 4.438 distance: 76 - 104: 11.153 distance: 77 - 78: 4.068 distance: 78 - 79: 3.852 distance: 78 - 80: 6.025 distance: 79 - 81: 5.977 distance: 80 - 82: 4.085 distance: 81 - 83: 5.698 distance: 82 - 83: 5.741 distance: 85 - 86: 9.437 distance: 85 - 88: 5.964 distance: 86 - 87: 4.746 distance: 87 - 111: 6.449 distance: 88 - 89: 3.769 distance: 89 - 90: 14.140 distance: 89 - 91: 11.315 distance: 92 - 93: 6.754 distance: 93 - 94: 8.092 distance: 94 - 95: 5.639 distance: 94 - 98: 5.165 distance: 95 - 116: 11.706 distance: 96 - 97: 5.717