Starting phenix.real_space_refine on Thu Jun 19 15:47:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fm6_50549/06_2025/9fm6_50549.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fm6_50549/06_2025/9fm6_50549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fm6_50549/06_2025/9fm6_50549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fm6_50549/06_2025/9fm6_50549.map" model { file = "/net/cci-nas-00/data/ceres_data/9fm6_50549/06_2025/9fm6_50549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fm6_50549/06_2025/9fm6_50549.cif" } resolution = 2.2 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= 0.068 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 56 5.16 5 C 14399 2.51 5 N 3899 2.21 5 O 4389 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22743 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3249 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 24, 'TRANS': 387} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 8.82, per 1000 atoms: 0.39 Number of scatterers: 22743 At special positions: 0 Unit cell: (175.13, 176.79, 116.2, 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 56 16.00 O 4389 8.00 N 3899 7.00 C 14399 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 164 " distance=2.04 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 164 " distance=2.04 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 164 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 164 " distance=2.04 Simple disulfide: pdb=" SG CYS D 159 " - pdb=" SG CYS D 164 " distance=2.04 Simple disulfide: pdb=" SG CYS G 159 " - pdb=" SG CYS G 164 " distance=2.04 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 164 " distance=2.04 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: 4.83 Conformation dependent library (CDL) restraints added in 2.8 seconds 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5236 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 16 sheets defined 19.4% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 34 through 41 Processing helix chain 'A' and resid 97 through 107 Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 372 through 381 removed outlier: 3.558A pdb=" N THR A 376 " --> pdb=" O ASP A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 393 Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 34 through 41 Processing helix chain 'B' and resid 97 through 107 Processing helix chain 'B' and resid 112 through 123 Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 372 through 381 removed outlier: 3.558A pdb=" N THR B 376 " --> pdb=" O ASP B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 393 Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 34 through 41 Processing helix chain 'C' and resid 97 through 107 Processing helix chain 'C' and resid 112 through 123 Processing helix chain 'C' and resid 354 through 361 Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 372 through 381 removed outlier: 3.558A pdb=" N THR C 376 " --> pdb=" O ASP C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 393 Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 34 through 41 Processing helix chain 'D' and resid 97 through 107 Processing helix chain 'D' and resid 112 through 123 Processing helix chain 'D' and resid 354 through 361 Processing helix chain 'D' and resid 364 through 368 Processing helix chain 'D' and resid 372 through 381 removed outlier: 3.558A pdb=" N THR D 376 " --> pdb=" O ASP D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 393 Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 27 through 34 Processing helix chain 'E' and resid 34 through 41 Processing helix chain 'E' and resid 97 through 107 Processing helix chain 'E' and resid 112 through 123 Processing helix chain 'E' and resid 354 through 361 Processing helix chain 'E' and resid 364 through 368 Processing helix chain 'E' and resid 372 through 381 removed outlier: 3.559A pdb=" N THR E 376 " --> pdb=" O ASP E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 393 Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 27 through 34 Processing helix chain 'F' and resid 34 through 41 Processing helix chain 'F' and resid 97 through 107 Processing helix chain 'F' and resid 112 through 123 Processing helix chain 'F' and resid 354 through 361 Processing helix chain 'F' and resid 364 through 368 Processing helix chain 'F' and resid 372 through 381 removed outlier: 3.558A pdb=" N THR F 376 " --> pdb=" O ASP F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 393 Processing helix chain 'G' and resid 5 through 9 Processing helix chain 'G' and resid 27 through 34 Processing helix chain 'G' and resid 34 through 41 Processing helix chain 'G' and resid 97 through 107 Processing helix chain 'G' and resid 112 through 123 Processing helix chain 'G' and resid 354 through 361 Processing helix chain 'G' and resid 364 through 368 Processing helix chain 'G' and resid 372 through 381 removed outlier: 3.559A pdb=" N THR G 376 " --> pdb=" O ASP G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 393 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 96 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 91 through 96 current: chain 'A' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 169 through 179 current: chain 'A' and resid 289 through 321 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 338 through 345 current: chain 'B' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 169 through 179 current: chain 'B' and resid 289 through 321 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 338 through 345 current: chain 'C' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 169 through 179 current: chain 'C' and resid 289 through 321 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 338 through 345 current: chain 'D' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 169 through 179 current: chain 'D' and resid 289 through 321 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 338 through 345 current: chain 'E' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 169 through 179 current: chain 'E' and resid 289 through 321 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 338 through 345 current: chain 'F' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 169 through 179 current: chain 'F' and resid 289 through 321 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 338 through 345 current: chain 'G' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 169 through 179 current: chain 'G' and resid 289 through 321 Processing sheet with id=AA4, first strand: chain 'A' and resid 215 through 247 removed outlier: 7.061A pdb=" N GLU A 252 " --> pdb=" O LYS G 244 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LYS G 244 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLU G 252 " --> pdb=" O LYS F 244 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LYS F 244 " --> pdb=" O GLU G 252 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLU F 252 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LYS E 244 " --> pdb=" O GLU F 252 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLU E 252 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LYS D 244 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLU D 252 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LYS C 244 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLU C 252 " --> pdb=" O LYS B 244 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LYS B 244 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLU B 252 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LYS A 244 " --> pdb=" O GLU B 252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'C' and resid 47 through 49 Processing sheet with id=AA9, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AB1, first strand: chain 'D' and resid 47 through 49 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AB3, first strand: chain 'E' and resid 47 through 49 Processing sheet with id=AB4, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AB5, first strand: chain 'F' and resid 47 through 49 Processing sheet with id=AB6, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AB7, first strand: chain 'G' and resid 47 through 49 875 hydrogen bonds defined for protein. 2478 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: 7.06 Time building geometry restraints manager: 5.89 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: 6571 1.34 - 1.46: 5980 1.46 - 1.59: 10759 1.59 - 1.71: 0 1.71 - 1.84: 91 Bond restraints: 23401 Sorted by residual: bond pdb=" C ARG F 336 " pdb=" O ARG F 336 " ideal model delta sigma weight residual 1.235 1.215 0.019 4.70e-03 4.53e+04 1.72e+01 bond pdb=" C ARG E 336 " pdb=" O ARG E 336 " ideal model delta sigma weight residual 1.235 1.216 0.019 4.70e-03 4.53e+04 1.70e+01 bond pdb=" C ARG C 336 " pdb=" O ARG C 336 " ideal model delta sigma weight residual 1.235 1.216 0.019 4.70e-03 4.53e+04 1.63e+01 bond pdb=" C ARG G 336 " pdb=" O ARG G 336 " ideal model delta sigma weight residual 1.235 1.216 0.019 4.70e-03 4.53e+04 1.59e+01 bond pdb=" C ARG B 336 " pdb=" O ARG B 336 " ideal model delta sigma weight residual 1.235 1.216 0.018 4.70e-03 4.53e+04 1.53e+01 ... (remaining 23396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 26155 1.32 - 2.64: 4310 2.64 - 3.96: 1126 3.96 - 5.28: 315 5.28 - 6.60: 49 Bond angle restraints: 31955 Sorted by residual: angle pdb=" N ALA B 310 " pdb=" CA ALA B 310 " pdb=" C ALA B 310 " ideal model delta sigma weight residual 108.96 115.22 -6.26 1.49e+00 4.50e-01 1.76e+01 angle pdb=" N ALA A 310 " pdb=" CA ALA A 310 " pdb=" C ALA A 310 " ideal model delta sigma weight residual 108.96 115.22 -6.26 1.49e+00 4.50e-01 1.76e+01 angle pdb=" N ALA D 310 " pdb=" CA ALA D 310 " pdb=" C ALA D 310 " ideal model delta sigma weight residual 108.96 115.19 -6.23 1.49e+00 4.50e-01 1.75e+01 angle pdb=" N ALA E 310 " pdb=" CA ALA E 310 " pdb=" C ALA E 310 " ideal model delta sigma weight residual 108.96 115.17 -6.21 1.49e+00 4.50e-01 1.74e+01 angle pdb=" N ALA G 310 " pdb=" CA ALA G 310 " pdb=" C ALA G 310 " ideal model delta sigma weight residual 108.96 115.17 -6.21 1.49e+00 4.50e-01 1.74e+01 ... (remaining 31950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13041 17.93 - 35.86: 378 35.86 - 53.80: 91 53.80 - 71.73: 42 71.73 - 89.66: 7 Dihedral angle restraints: 13559 sinusoidal: 5313 harmonic: 8246 Sorted by residual: dihedral pdb=" CA ASP G 311 " pdb=" CB ASP G 311 " pdb=" CG ASP G 311 " pdb=" OD1 ASP G 311 " ideal model delta sinusoidal sigma weight residual -30.00 -86.40 56.40 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASP C 311 " pdb=" CB ASP C 311 " pdb=" CG ASP C 311 " pdb=" OD1 ASP C 311 " ideal model delta sinusoidal sigma weight residual -30.00 -86.39 56.39 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASP D 311 " pdb=" CB ASP D 311 " pdb=" CG ASP D 311 " pdb=" OD1 ASP D 311 " ideal model delta sinusoidal sigma weight residual -30.00 -86.39 56.39 1 2.00e+01 2.50e-03 1.07e+01 ... (remaining 13556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1820 0.039 - 0.078: 959 0.078 - 0.117: 417 0.117 - 0.156: 143 0.156 - 0.195: 14 Chirality restraints: 3353 Sorted by residual: chirality pdb=" CA ILE G 416 " pdb=" N ILE G 416 " pdb=" C ILE G 416 " pdb=" CB ILE G 416 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.47e-01 chirality pdb=" CA ILE B 416 " pdb=" N ILE B 416 " pdb=" C ILE B 416 " pdb=" CB ILE B 416 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.39e-01 chirality pdb=" CA ILE F 416 " pdb=" N ILE F 416 " pdb=" C ILE F 416 " pdb=" CB ILE F 416 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.38e-01 ... (remaining 3350 not shown) Planarity restraints: 4151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 249 " -0.021 2.00e-02 2.50e+03 4.19e-02 1.75e+01 pdb=" C LEU D 249 " 0.072 2.00e-02 2.50e+03 pdb=" O LEU D 249 " -0.027 2.00e-02 2.50e+03 pdb=" N VAL D 250 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 249 " -0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C LEU B 249 " 0.072 2.00e-02 2.50e+03 pdb=" O LEU B 249 " -0.027 2.00e-02 2.50e+03 pdb=" N VAL B 250 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 249 " -0.021 2.00e-02 2.50e+03 4.18e-02 1.74e+01 pdb=" C LEU E 249 " 0.072 2.00e-02 2.50e+03 pdb=" O LEU E 249 " -0.027 2.00e-02 2.50e+03 pdb=" N VAL E 250 " -0.024 2.00e-02 2.50e+03 ... (remaining 4148 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 11277 2.99 - 3.47: 19575 3.47 - 3.95: 38037 3.95 - 4.42: 40659 4.42 - 4.90: 68884 Nonbonded interactions: 178432 Sorted by model distance: nonbonded pdb=" N ASP G 334 " pdb=" OD1 ASP G 334 " model vdw 2.516 3.120 nonbonded pdb=" N ASP E 334 " pdb=" OD1 ASP E 334 " model vdw 2.516 3.120 nonbonded pdb=" N ASP C 334 " pdb=" OD1 ASP C 334 " model vdw 2.516 3.120 nonbonded pdb=" N ASP D 334 " pdb=" OD1 ASP D 334 " model vdw 2.516 3.120 nonbonded pdb=" N ASP F 334 " pdb=" OD1 ASP F 334 " model vdw 2.517 3.120 ... (remaining 178427 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.900 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: 0.020 Extract box with map and model: 0.970 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 44.110 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:13.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 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 : 0.009 0.069 23408 Z= 0.474 Angle : 1.156 6.599 31969 Z= 0.728 Chirality : 0.056 0.195 3353 Planarity : 0.009 0.128 4151 Dihedral : 10.566 89.660 8302 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.57 % Allowed : 0.29 % Favored : 99.14 % 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: 1.39 (0.15), residues: 2856 helix: -0.37 (0.19), residues: 497 sheet: 2.35 (0.15), residues: 994 loop : 0.41 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 370 HIS 0.004 0.002 HIS B 186 PHE 0.029 0.004 PHE B 321 TYR 0.029 0.004 TYR D 61 ARG 0.011 0.001 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.17054 ( 875) hydrogen bonds : angle 6.91411 ( 2478) SS BOND : bond 0.00915 ( 7) SS BOND : angle 2.52641 ( 14) covalent geometry : bond 0.00853 (23401) covalent geometry : angle 1.15547 (31955) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 379 time to evaluate : 2.381 Fit side-chains REVERT: A 2 GLU cc_start: 0.6277 (mm-30) cc_final: 0.5308 (tt0) REVERT: A 30 GLU cc_start: 0.5674 (mt-10) cc_final: 0.4712 (mm-30) REVERT: A 57 MET cc_start: 0.5888 (mtp) cc_final: 0.5640 (mtm) REVERT: A 114 LYS cc_start: 0.7161 (mmmt) cc_final: 0.6573 (mptt) REVERT: A 135 TYR cc_start: 0.6002 (m-80) cc_final: 0.5754 (m-80) REVERT: A 147 ASP cc_start: 0.6741 (m-30) cc_final: 0.6371 (t0) REVERT: A 171 LYS cc_start: 0.7922 (mttt) cc_final: 0.6602 (tptm) REVERT: A 258 GLU cc_start: 0.7588 (tt0) cc_final: 0.7341 (tt0) REVERT: A 259 ILE cc_start: 0.7665 (mm) cc_final: 0.7341 (mm) REVERT: A 378 GLN cc_start: 0.7017 (mt0) cc_final: 0.6214 (mm110) REVERT: A 385 MET cc_start: 0.7902 (mmm) cc_final: 0.7196 (mmm) REVERT: A 408 SER cc_start: 0.8268 (m) cc_final: 0.8056 (t) REVERT: B 2 GLU cc_start: 0.6345 (mm-30) cc_final: 0.5875 (mt-10) REVERT: B 30 GLU cc_start: 0.5601 (mt-10) cc_final: 0.4598 (mm-30) REVERT: B 42 MET cc_start: 0.3774 (mtp) cc_final: 0.3563 (mtp) REVERT: B 114 LYS cc_start: 0.7062 (mmmt) cc_final: 0.6471 (mptt) REVERT: B 147 ASP cc_start: 0.6694 (m-30) cc_final: 0.6330 (t0) REVERT: B 171 LYS cc_start: 0.7725 (mttt) cc_final: 0.6290 (tptm) REVERT: B 258 GLU cc_start: 0.7480 (tt0) cc_final: 0.7188 (tt0) REVERT: B 378 GLN cc_start: 0.6805 (mt0) cc_final: 0.5710 (mp10) REVERT: C 2 GLU cc_start: 0.6227 (mm-30) cc_final: 0.5648 (mt-10) REVERT: C 30 GLU cc_start: 0.5586 (mt-10) cc_final: 0.4667 (mm-30) REVERT: C 114 LYS cc_start: 0.7024 (mmmt) cc_final: 0.6424 (mptt) REVERT: C 145 ASP cc_start: 0.7116 (t0) cc_final: 0.6895 (t70) REVERT: C 147 ASP cc_start: 0.6718 (m-30) cc_final: 0.6340 (t0) REVERT: C 171 LYS cc_start: 0.7704 (mttt) cc_final: 0.6211 (tptp) REVERT: C 299 LYS cc_start: 0.8049 (mttt) cc_final: 0.7773 (mttt) REVERT: C 323 ARG cc_start: 0.6913 (mtm180) cc_final: 0.6645 (mtm-85) REVERT: C 378 GLN cc_start: 0.6595 (mt0) cc_final: 0.5772 (mm110) REVERT: C 407 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7511 (mt-10) REVERT: D 2 GLU cc_start: 0.6468 (mm-30) cc_final: 0.6073 (mm-30) REVERT: D 57 MET cc_start: 0.6171 (mtp) cc_final: 0.5924 (mtm) REVERT: D 114 LYS cc_start: 0.7023 (mmmt) cc_final: 0.6388 (mptt) REVERT: D 147 ASP cc_start: 0.6777 (m-30) cc_final: 0.6408 (t0) REVERT: D 171 LYS cc_start: 0.7754 (mttt) cc_final: 0.6235 (tptm) REVERT: D 243 ASN cc_start: 0.7114 (m110) cc_final: 0.6894 (m110) REVERT: D 378 GLN cc_start: 0.6737 (mt0) cc_final: 0.5972 (mm110) REVERT: D 408 SER cc_start: 0.8239 (m) cc_final: 0.8031 (t) REVERT: E 2 GLU cc_start: 0.6214 (mm-30) cc_final: 0.5732 (mt-10) REVERT: E 30 GLU cc_start: 0.5471 (mt-10) cc_final: 0.4561 (mm-30) REVERT: E 57 MET cc_start: 0.6043 (mtp) cc_final: 0.5818 (mtm) REVERT: E 114 LYS cc_start: 0.7030 (mmmt) cc_final: 0.6367 (mptt) REVERT: E 147 ASP cc_start: 0.6733 (m-30) cc_final: 0.6196 (t0) REVERT: E 171 LYS cc_start: 0.7705 (mttt) cc_final: 0.6277 (tptp) REVERT: E 258 GLU cc_start: 0.7503 (tt0) cc_final: 0.7162 (tt0) REVERT: E 378 GLN cc_start: 0.6810 (mt0) cc_final: 0.5958 (mm110) REVERT: E 385 MET cc_start: 0.7600 (mmm) cc_final: 0.7207 (mmm) REVERT: E 408 SER cc_start: 0.8263 (m) cc_final: 0.8038 (t) REVERT: F 2 GLU cc_start: 0.6196 (mm-30) cc_final: 0.5369 (tt0) REVERT: F 30 GLU cc_start: 0.5894 (mt-10) cc_final: 0.4799 (mm-30) REVERT: F 57 MET cc_start: 0.6155 (mtp) cc_final: 0.5925 (mtp) REVERT: F 114 LYS cc_start: 0.7313 (mmmt) cc_final: 0.6626 (mptt) REVERT: F 147 ASP cc_start: 0.6635 (m-30) cc_final: 0.6249 (t0) REVERT: F 171 LYS cc_start: 0.7869 (mttt) cc_final: 0.6515 (tptm) REVERT: F 258 GLU cc_start: 0.7534 (tt0) cc_final: 0.7231 (tt0) REVERT: F 307 GLU cc_start: 0.7989 (pt0) cc_final: 0.7773 (pt0) REVERT: F 323 ARG cc_start: 0.7136 (mtm180) cc_final: 0.6849 (mtp180) REVERT: F 378 GLN cc_start: 0.6710 (mt0) cc_final: 0.5849 (mm110) REVERT: G 2 GLU cc_start: 0.6445 (mm-30) cc_final: 0.5839 (mt-10) REVERT: G 30 GLU cc_start: 0.5569 (mt-10) cc_final: 0.4625 (mm-30) REVERT: G 114 LYS cc_start: 0.7090 (mmmt) cc_final: 0.6458 (mptt) REVERT: G 147 ASP cc_start: 0.6758 (m-30) cc_final: 0.6388 (t0) REVERT: G 171 LYS cc_start: 0.7859 (mttt) cc_final: 0.6476 (tptp) REVERT: G 378 GLN cc_start: 0.6647 (mt0) cc_final: 0.5594 (mp10) outliers start: 14 outliers final: 0 residues processed: 393 average time/residue: 1.5235 time to fit residues: 672.3040 Evaluate side-chains 242 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 0.5980 chunk 217 optimal weight: 0.0010 chunk 120 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 224 optimal weight: 0.8980 chunk 87 optimal weight: 30.0000 chunk 136 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 260 optimal weight: 6.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN B 338 ASN C 174 ASN C 338 ASN D 174 ASN D 231 ASN D 338 ASN E 174 ASN E 243 ASN F 174 ASN G 243 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.162860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.133455 restraints weight = 19344.515| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.37 r_work: 0.3206 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 23408 Z= 0.187 Angle : 0.613 4.449 31969 Z= 0.352 Chirality : 0.047 0.149 3353 Planarity : 0.004 0.031 4151 Dihedral : 4.819 16.539 3129 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.78 % Allowed : 4.42 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.15), residues: 2856 helix: 0.85 (0.21), residues: 497 sheet: 1.74 (0.14), residues: 1176 loop : 0.41 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 370 HIS 0.004 0.001 HIS F 186 PHE 0.016 0.002 PHE G 321 TYR 0.018 0.002 TYR G 61 ARG 0.003 0.001 ARG D 220 Details of bonding type rmsd hydrogen bonds : bond 0.05678 ( 875) hydrogen bonds : angle 5.43335 ( 2478) SS BOND : bond 0.00420 ( 7) SS BOND : angle 1.61974 ( 14) covalent geometry : bond 0.00291 (23401) covalent geometry : angle 0.61230 (31955) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 258 time to evaluate : 2.505 Fit side-chains REVERT: A 2 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6847 (tt0) REVERT: A 42 MET cc_start: 0.4390 (mtp) cc_final: 0.4117 (mtp) REVERT: A 114 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8404 (mptt) REVERT: A 138 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7324 (mm-30) REVERT: A 171 LYS cc_start: 0.8799 (mttt) cc_final: 0.8177 (tptp) REVERT: A 378 GLN cc_start: 0.7756 (mt0) cc_final: 0.7504 (mm110) REVERT: A 385 MET cc_start: 0.8921 (mmm) cc_final: 0.8449 (mmm) REVERT: B 2 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6782 (tt0) REVERT: B 114 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8393 (mptt) REVERT: B 138 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7028 (mm-30) REVERT: B 171 LYS cc_start: 0.8823 (mttt) cc_final: 0.8116 (tptp) REVERT: B 378 GLN cc_start: 0.7869 (mt0) cc_final: 0.7492 (mp10) REVERT: C 114 LYS cc_start: 0.8619 (mmmt) cc_final: 0.8409 (mptt) REVERT: C 171 LYS cc_start: 0.8799 (mttt) cc_final: 0.8148 (tptm) REVERT: C 378 GLN cc_start: 0.7656 (mt0) cc_final: 0.7401 (mm110) REVERT: D 171 LYS cc_start: 0.8859 (mttt) cc_final: 0.8154 (tptp) REVERT: E 114 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8404 (mptt) REVERT: E 138 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7045 (mm-30) REVERT: E 171 LYS cc_start: 0.8881 (mttt) cc_final: 0.8119 (tptm) REVERT: E 385 MET cc_start: 0.8851 (mmm) cc_final: 0.8530 (mmm) REVERT: F 2 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6874 (tt0) REVERT: F 114 LYS cc_start: 0.8609 (mmmt) cc_final: 0.8353 (mptt) REVERT: F 138 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7072 (mm-30) REVERT: F 171 LYS cc_start: 0.8825 (mttt) cc_final: 0.8187 (tptp) REVERT: F 378 GLN cc_start: 0.7720 (mt0) cc_final: 0.7454 (mm110) REVERT: G 42 MET cc_start: 0.4506 (mtp) cc_final: 0.4191 (mtp) REVERT: G 114 LYS cc_start: 0.8559 (mmmt) cc_final: 0.8333 (mptt) REVERT: G 171 LYS cc_start: 0.8812 (mttt) cc_final: 0.8166 (tptp) REVERT: G 254 GLU cc_start: 0.7705 (tt0) cc_final: 0.7474 (tt0) REVERT: G 378 GLN cc_start: 0.7747 (mt0) cc_final: 0.7469 (mp10) outliers start: 19 outliers final: 7 residues processed: 276 average time/residue: 1.2627 time to fit residues: 401.3362 Evaluate side-chains 235 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 224 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain F residue 138 GLU Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain G residue 408 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 259 optimal weight: 8.9990 chunk 96 optimal weight: 0.1980 chunk 195 optimal weight: 9.9990 chunk 146 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 239 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN A 243 ASN B 174 ASN B 338 ASN C 174 ASN C 231 ASN C 338 ASN D 174 ASN D 338 ASN E 174 ASN E 338 ASN F 174 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.163615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.131399 restraints weight = 19322.718| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.20 r_work: 0.3263 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 23408 Z= 0.211 Angle : 0.642 5.198 31969 Z= 0.372 Chirality : 0.049 0.149 3353 Planarity : 0.005 0.038 4151 Dihedral : 5.083 18.104 3129 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.39 % Allowed : 5.24 % Favored : 93.37 % 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: 1.19 (0.15), residues: 2856 helix: 1.13 (0.22), residues: 497 sheet: 1.24 (0.14), residues: 1204 loop : 0.26 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 370 HIS 0.008 0.002 HIS E 186 PHE 0.017 0.003 PHE G 321 TYR 0.020 0.002 TYR A 61 ARG 0.004 0.001 ARG E 282 Details of bonding type rmsd hydrogen bonds : bond 0.06454 ( 875) hydrogen bonds : angle 5.19094 ( 2478) SS BOND : bond 0.00271 ( 7) SS BOND : angle 0.96820 ( 14) covalent geometry : bond 0.00349 (23401) covalent geometry : angle 0.64182 (31955) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 243 time to evaluate : 2.449 Fit side-chains REVERT: A 2 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6787 (tt0) REVERT: A 30 GLU cc_start: 0.6809 (mt-10) cc_final: 0.5902 (mm-30) REVERT: A 42 MET cc_start: 0.4426 (mtp) cc_final: 0.4130 (mtp) REVERT: A 114 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8416 (mptt) REVERT: A 171 LYS cc_start: 0.8877 (mttt) cc_final: 0.8230 (tptp) REVERT: A 258 GLU cc_start: 0.8468 (tt0) cc_final: 0.8232 (tt0) REVERT: A 378 GLN cc_start: 0.7961 (mt0) cc_final: 0.7635 (mm110) REVERT: A 385 MET cc_start: 0.8934 (mmm) cc_final: 0.8405 (mmm) REVERT: B 2 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6764 (tt0) REVERT: B 10 ARG cc_start: 0.2896 (OUTLIER) cc_final: 0.2108 (ptt90) REVERT: B 42 MET cc_start: 0.4222 (mtp) cc_final: 0.3758 (mtm) REVERT: B 114 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8419 (mptt) REVERT: B 171 LYS cc_start: 0.8871 (mttt) cc_final: 0.8134 (tptm) REVERT: C 114 LYS cc_start: 0.8660 (mmmt) cc_final: 0.8432 (mptt) REVERT: C 171 LYS cc_start: 0.8837 (mttt) cc_final: 0.8140 (tptm) REVERT: C 242 LYS cc_start: 0.8230 (ttmm) cc_final: 0.7803 (ttmt) REVERT: C 378 GLN cc_start: 0.7910 (mt0) cc_final: 0.7538 (mm110) REVERT: D 2 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6682 (tt0) REVERT: D 171 LYS cc_start: 0.8881 (mttt) cc_final: 0.8145 (tptm) REVERT: E 42 MET cc_start: 0.4326 (mtp) cc_final: 0.3919 (mtp) REVERT: E 114 LYS cc_start: 0.8656 (mmmt) cc_final: 0.8405 (mptt) REVERT: E 138 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7053 (mm-30) REVERT: E 171 LYS cc_start: 0.8896 (mttt) cc_final: 0.8126 (tptm) REVERT: E 385 MET cc_start: 0.8887 (mmm) cc_final: 0.8375 (mmm) REVERT: F 2 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6843 (tt0) REVERT: F 114 LYS cc_start: 0.8636 (mmmt) cc_final: 0.8362 (mptt) REVERT: F 171 LYS cc_start: 0.8877 (mttt) cc_final: 0.8231 (tptm) REVERT: F 378 GLN cc_start: 0.7911 (mt0) cc_final: 0.7581 (mm110) REVERT: G 42 MET cc_start: 0.4572 (mtp) cc_final: 0.4298 (mtp) REVERT: G 114 LYS cc_start: 0.8553 (mmmt) cc_final: 0.8347 (mptt) REVERT: G 138 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7463 (mm-30) REVERT: G 171 LYS cc_start: 0.8875 (mttt) cc_final: 0.8147 (tptp) REVERT: G 254 GLU cc_start: 0.7818 (tt0) cc_final: 0.7577 (tt0) REVERT: G 378 GLN cc_start: 0.7860 (mt0) cc_final: 0.7439 (mp10) outliers start: 34 outliers final: 18 residues processed: 265 average time/residue: 1.2654 time to fit residues: 386.9143 Evaluate side-chains 253 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 231 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 138 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 206 optimal weight: 9.9990 chunk 14 optimal weight: 0.5980 chunk 168 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 209 optimal weight: 0.5980 chunk 236 optimal weight: 9.9990 chunk 213 optimal weight: 7.9990 chunk 271 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 204 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN B 231 ASN B 338 ASN B 378 GLN C 174 ASN C 231 ASN C 338 ASN D 174 ASN D 231 ASN D 338 ASN E 174 ASN E 338 ASN F 174 ASN F 231 ASN F 341 HIS G 338 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.162018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.129959 restraints weight = 19563.118| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.58 r_work: 0.3282 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 23408 Z= 0.230 Angle : 0.673 5.263 31969 Z= 0.388 Chirality : 0.051 0.154 3353 Planarity : 0.005 0.040 4151 Dihedral : 5.251 18.543 3129 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.51 % Allowed : 5.57 % Favored : 92.92 % 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: 0.90 (0.15), residues: 2856 helix: 0.87 (0.22), residues: 497 sheet: 1.20 (0.14), residues: 1176 loop : -0.05 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 370 HIS 0.010 0.002 HIS F 186 PHE 0.018 0.003 PHE G 321 TYR 0.016 0.002 TYR B 76 ARG 0.005 0.001 ARG F 282 Details of bonding type rmsd hydrogen bonds : bond 0.06736 ( 875) hydrogen bonds : angle 5.21269 ( 2478) SS BOND : bond 0.00342 ( 7) SS BOND : angle 0.94120 ( 14) covalent geometry : bond 0.00389 (23401) covalent geometry : angle 0.67318 (31955) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 2.519 Fit side-chains REVERT: A 2 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6826 (tt0) REVERT: A 42 MET cc_start: 0.4545 (mtp) cc_final: 0.4238 (mtp) REVERT: A 114 LYS cc_start: 0.8576 (mmmt) cc_final: 0.8367 (mptt) REVERT: A 138 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7385 (mm-30) REVERT: A 171 LYS cc_start: 0.8808 (mttt) cc_final: 0.8144 (tptm) REVERT: A 258 GLU cc_start: 0.8330 (tt0) cc_final: 0.8073 (tt0) REVERT: A 378 GLN cc_start: 0.7918 (mt0) cc_final: 0.7508 (mm110) REVERT: A 385 MET cc_start: 0.8908 (mmm) cc_final: 0.8366 (mmm) REVERT: B 2 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6720 (tt0) REVERT: B 10 ARG cc_start: 0.2925 (OUTLIER) cc_final: 0.2191 (ptt90) REVERT: B 42 MET cc_start: 0.4359 (mtp) cc_final: 0.3719 (mtp) REVERT: B 114 LYS cc_start: 0.8570 (mmmt) cc_final: 0.8315 (mptt) REVERT: B 138 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.6926 (mm-30) REVERT: B 171 LYS cc_start: 0.8758 (mttt) cc_final: 0.8011 (tptm) REVERT: B 277 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8112 (tt) REVERT: B 378 GLN cc_start: 0.7914 (tp40) cc_final: 0.7662 (mp10) REVERT: C 114 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8366 (mptt) REVERT: C 171 LYS cc_start: 0.8770 (mttt) cc_final: 0.8047 (tptm) REVERT: C 242 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7797 (ttmt) REVERT: C 378 GLN cc_start: 0.7828 (mt0) cc_final: 0.7454 (mm110) REVERT: D 2 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6572 (tt0) REVERT: D 171 LYS cc_start: 0.8790 (mttt) cc_final: 0.8039 (tptm) REVERT: D 242 LYS cc_start: 0.8326 (ttmm) cc_final: 0.8113 (ttmt) REVERT: E 42 MET cc_start: 0.4421 (mtp) cc_final: 0.4021 (mtp) REVERT: E 114 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8337 (mptt) REVERT: E 138 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.6947 (mm-30) REVERT: E 171 LYS cc_start: 0.8792 (mttt) cc_final: 0.8008 (tptm) REVERT: E 385 MET cc_start: 0.8845 (mmm) cc_final: 0.8355 (mmm) REVERT: F 2 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6875 (tt0) REVERT: F 114 LYS cc_start: 0.8538 (mmmt) cc_final: 0.8290 (mptt) REVERT: F 138 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7175 (mm-30) REVERT: F 171 LYS cc_start: 0.8793 (mttt) cc_final: 0.8134 (tptm) REVERT: F 378 GLN cc_start: 0.7932 (mt0) cc_final: 0.7481 (mm110) REVERT: G 42 MET cc_start: 0.4478 (mtp) cc_final: 0.4191 (mtp) REVERT: G 57 MET cc_start: 0.6739 (mtm) cc_final: 0.6287 (mtp) REVERT: G 114 LYS cc_start: 0.8503 (mmmt) cc_final: 0.8262 (mptt) REVERT: G 138 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7349 (mm-30) REVERT: G 171 LYS cc_start: 0.8811 (mttt) cc_final: 0.8073 (tptp) REVERT: G 378 GLN cc_start: 0.7914 (mt0) cc_final: 0.7535 (mm110) outliers start: 37 outliers final: 17 residues processed: 259 average time/residue: 1.2640 time to fit residues: 376.9564 Evaluate side-chains 251 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 226 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 138 GLU Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 138 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 156 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 202 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 249 optimal weight: 0.0970 chunk 47 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN B 338 ASN C 174 ASN C 231 ASN C 338 ASN D 231 ASN D 338 ASN E 174 ASN E 231 ASN F 174 ASN F 231 ASN G 338 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.160648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128367 restraints weight = 19337.837| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.39 r_work: 0.3264 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 23408 Z= 0.262 Angle : 0.731 6.159 31969 Z= 0.420 Chirality : 0.053 0.175 3353 Planarity : 0.006 0.041 4151 Dihedral : 5.432 18.903 3129 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.96 % Allowed : 5.53 % Favored : 92.51 % 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: 0.73 (0.15), residues: 2856 helix: 0.63 (0.21), residues: 497 sheet: 1.17 (0.14), residues: 1176 loop : -0.22 (0.16), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 370 HIS 0.009 0.002 HIS A 186 PHE 0.020 0.003 PHE A 321 TYR 0.017 0.003 TYR A 233 ARG 0.005 0.001 ARG G 282 Details of bonding type rmsd hydrogen bonds : bond 0.07368 ( 875) hydrogen bonds : angle 5.28408 ( 2478) SS BOND : bond 0.00347 ( 7) SS BOND : angle 0.91552 ( 14) covalent geometry : bond 0.00459 (23401) covalent geometry : angle 0.73053 (31955) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 231 time to evaluate : 2.322 Fit side-chains REVERT: A 2 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6830 (tt0) REVERT: A 42 MET cc_start: 0.4717 (mtp) cc_final: 0.4385 (mtp) REVERT: A 114 LYS cc_start: 0.8559 (mmmt) cc_final: 0.8351 (mptt) REVERT: A 138 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7428 (mm-30) REVERT: A 171 LYS cc_start: 0.8808 (mttt) cc_final: 0.8131 (tptm) REVERT: A 242 LYS cc_start: 0.8337 (ttmm) cc_final: 0.8037 (ttmt) REVERT: A 258 GLU cc_start: 0.8316 (tt0) cc_final: 0.8075 (tt0) REVERT: A 378 GLN cc_start: 0.7974 (mt0) cc_final: 0.7555 (mm110) REVERT: B 2 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6747 (tt0) REVERT: B 10 ARG cc_start: 0.2716 (OUTLIER) cc_final: 0.2015 (ptt90) REVERT: B 42 MET cc_start: 0.4429 (mtp) cc_final: 0.3902 (mtp) REVERT: B 114 LYS cc_start: 0.8568 (mmmt) cc_final: 0.8304 (mptt) REVERT: B 171 LYS cc_start: 0.8730 (mttt) cc_final: 0.7993 (tptp) REVERT: B 277 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8161 (tt) REVERT: C 114 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8359 (mptt) REVERT: C 171 LYS cc_start: 0.8788 (mttt) cc_final: 0.8046 (tptm) REVERT: C 242 LYS cc_start: 0.8283 (ttmm) cc_final: 0.7885 (ttmt) REVERT: C 378 GLN cc_start: 0.7871 (mt0) cc_final: 0.7414 (mm110) REVERT: D 2 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6561 (tt0) REVERT: D 138 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7201 (mm-30) REVERT: D 171 LYS cc_start: 0.8770 (mttt) cc_final: 0.8019 (tptm) REVERT: D 242 LYS cc_start: 0.8349 (ttmm) cc_final: 0.8107 (ttmt) REVERT: D 277 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8454 (tt) REVERT: E 42 MET cc_start: 0.4451 (mtp) cc_final: 0.4032 (mtp) REVERT: E 114 LYS cc_start: 0.8604 (mmmt) cc_final: 0.8318 (mptt) REVERT: E 138 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.6959 (mm-30) REVERT: E 171 LYS cc_start: 0.8797 (mttt) cc_final: 0.8015 (tptm) REVERT: E 277 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8472 (tp) REVERT: E 385 MET cc_start: 0.8836 (mmm) cc_final: 0.8363 (mmm) REVERT: F 2 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6867 (tt0) REVERT: F 114 LYS cc_start: 0.8554 (mmmt) cc_final: 0.8285 (mptt) REVERT: F 171 LYS cc_start: 0.8835 (mttt) cc_final: 0.8147 (tptm) REVERT: F 378 GLN cc_start: 0.8026 (mt0) cc_final: 0.7566 (mm110) REVERT: G 10 ARG cc_start: 0.2795 (OUTLIER) cc_final: 0.2451 (ptt90) REVERT: G 42 MET cc_start: 0.4534 (mtp) cc_final: 0.4234 (mtp) REVERT: G 57 MET cc_start: 0.6704 (mtm) cc_final: 0.6266 (mtp) REVERT: G 114 LYS cc_start: 0.8496 (mmmt) cc_final: 0.8248 (mptt) REVERT: G 138 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7359 (mm-30) REVERT: G 171 LYS cc_start: 0.8839 (mttt) cc_final: 0.8075 (tptp) REVERT: G 254 GLU cc_start: 0.7811 (tt0) cc_final: 0.7560 (tt0) REVERT: G 378 GLN cc_start: 0.7922 (mt0) cc_final: 0.7482 (mm110) outliers start: 48 outliers final: 20 residues processed: 267 average time/residue: 1.2623 time to fit residues: 388.6367 Evaluate side-chains 257 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 138 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 106 optimal weight: 6.9990 chunk 245 optimal weight: 9.9990 chunk 146 optimal weight: 0.5980 chunk 175 optimal weight: 20.0000 chunk 226 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 256 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN B 338 ASN B 341 HIS C 174 ASN C 231 ASN D 231 ASN D 338 ASN E 174 ASN E 231 ASN E 338 ASN F 174 ASN F 231 ASN G 338 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.158906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.126846 restraints weight = 19308.590| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.37 r_work: 0.3243 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 23408 Z= 0.321 Angle : 0.839 7.484 31969 Z= 0.481 Chirality : 0.057 0.227 3353 Planarity : 0.006 0.050 4151 Dihedral : 5.760 20.131 3129 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.92 % Allowed : 5.89 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.14), residues: 2856 helix: 0.18 (0.20), residues: 497 sheet: 1.16 (0.14), residues: 1176 loop : -0.36 (0.16), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP G 370 HIS 0.008 0.002 HIS F 186 PHE 0.022 0.004 PHE G 321 TYR 0.022 0.004 TYR A 233 ARG 0.008 0.001 ARG G 282 Details of bonding type rmsd hydrogen bonds : bond 0.08392 ( 875) hydrogen bonds : angle 5.45800 ( 2478) SS BOND : bond 0.00388 ( 7) SS BOND : angle 1.12118 ( 14) covalent geometry : bond 0.00588 (23401) covalent geometry : angle 0.83930 (31955) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 228 time to evaluate : 2.382 Fit side-chains REVERT: A 42 MET cc_start: 0.4743 (mtp) cc_final: 0.4400 (mtp) REVERT: A 114 LYS cc_start: 0.8608 (mmmt) cc_final: 0.8387 (mptt) REVERT: A 138 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7442 (mm-30) REVERT: A 171 LYS cc_start: 0.8815 (mttt) cc_final: 0.8135 (tptp) REVERT: A 242 LYS cc_start: 0.8332 (ttmm) cc_final: 0.8037 (ttmt) REVERT: A 258 GLU cc_start: 0.8364 (tt0) cc_final: 0.8127 (tt0) REVERT: A 378 GLN cc_start: 0.8048 (mt0) cc_final: 0.7598 (mm110) REVERT: B 2 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6749 (tt0) REVERT: B 10 ARG cc_start: 0.2748 (OUTLIER) cc_final: 0.2010 (ptt90) REVERT: B 42 MET cc_start: 0.4496 (mtp) cc_final: 0.3894 (mtp) REVERT: B 114 LYS cc_start: 0.8587 (mmmt) cc_final: 0.8323 (mptt) REVERT: B 138 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7003 (mm-30) REVERT: B 171 LYS cc_start: 0.8753 (mttt) cc_final: 0.7992 (tptp) REVERT: B 277 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8259 (tt) REVERT: C 114 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8391 (mptt) REVERT: C 171 LYS cc_start: 0.8812 (mttt) cc_final: 0.8073 (tptm) REVERT: C 378 GLN cc_start: 0.7968 (mt0) cc_final: 0.7518 (mm110) REVERT: D 2 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6563 (tt0) REVERT: D 138 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7240 (mm-30) REVERT: D 171 LYS cc_start: 0.8799 (mttt) cc_final: 0.8023 (tptp) REVERT: D 242 LYS cc_start: 0.8405 (ttmm) cc_final: 0.8118 (ttmt) REVERT: E 42 MET cc_start: 0.4580 (mtp) cc_final: 0.4037 (mtp) REVERT: E 114 LYS cc_start: 0.8634 (mmmt) cc_final: 0.8352 (mptt) REVERT: E 138 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.6994 (mm-30) REVERT: E 171 LYS cc_start: 0.8818 (mttt) cc_final: 0.8025 (tptm) REVERT: F 10 ARG cc_start: 0.2388 (OUTLIER) cc_final: 0.2142 (ptt180) REVERT: F 114 LYS cc_start: 0.8534 (mmmt) cc_final: 0.8288 (mptt) REVERT: F 138 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7185 (mm-30) REVERT: F 171 LYS cc_start: 0.8870 (mttt) cc_final: 0.8175 (tptp) REVERT: F 378 GLN cc_start: 0.8072 (mt0) cc_final: 0.7579 (mm110) REVERT: G 10 ARG cc_start: 0.3007 (OUTLIER) cc_final: 0.2639 (ptt90) REVERT: G 42 MET cc_start: 0.4531 (mtp) cc_final: 0.4230 (mtp) REVERT: G 57 MET cc_start: 0.6763 (mtm) cc_final: 0.6328 (mtp) REVERT: G 114 LYS cc_start: 0.8506 (mmmt) cc_final: 0.8270 (mptt) REVERT: G 138 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7384 (mm-30) REVERT: G 171 LYS cc_start: 0.8844 (mttt) cc_final: 0.8087 (tptp) REVERT: G 378 GLN cc_start: 0.7917 (mt0) cc_final: 0.7525 (mm110) outliers start: 47 outliers final: 22 residues processed: 265 average time/residue: 1.3050 time to fit residues: 402.0706 Evaluate side-chains 256 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 223 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain F residue 10 ARG Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 138 GLU Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 138 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 152 optimal weight: 0.2980 chunk 178 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 213 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 142 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN B 338 ASN C 174 ASN C 231 ASN D 231 ASN D 338 ASN E 174 ASN E 231 ASN F 174 ASN F 231 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.163329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.131851 restraints weight = 19619.068| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.31 r_work: 0.3311 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 23408 Z= 0.182 Angle : 0.594 5.247 31969 Z= 0.340 Chirality : 0.047 0.149 3353 Planarity : 0.004 0.031 4151 Dihedral : 5.077 18.592 3129 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.86 % Allowed : 7.25 % Favored : 91.90 % 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: 0.68 (0.15), residues: 2856 helix: 0.80 (0.21), residues: 497 sheet: 1.12 (0.14), residues: 1176 loop : -0.33 (0.16), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 370 HIS 0.004 0.001 HIS E 186 PHE 0.013 0.002 PHE D 321 TYR 0.013 0.002 TYR C 215 ARG 0.002 0.000 ARG G 282 Details of bonding type rmsd hydrogen bonds : bond 0.05486 ( 875) hydrogen bonds : angle 5.11723 ( 2478) SS BOND : bond 0.00112 ( 7) SS BOND : angle 0.70597 ( 14) covalent geometry : bond 0.00297 (23401) covalent geometry : angle 0.59379 (31955) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 234 time to evaluate : 2.539 Fit side-chains REVERT: A 30 GLU cc_start: 0.6589 (mt-10) cc_final: 0.5666 (mm-30) REVERT: A 42 MET cc_start: 0.4576 (mtp) cc_final: 0.4223 (mtp) REVERT: A 114 LYS cc_start: 0.8579 (mmmt) cc_final: 0.8362 (mptt) REVERT: A 171 LYS cc_start: 0.8812 (mttt) cc_final: 0.8122 (tptm) REVERT: A 242 LYS cc_start: 0.8180 (ttmm) cc_final: 0.7911 (ttpt) REVERT: A 378 GLN cc_start: 0.7961 (mt0) cc_final: 0.7527 (mm110) REVERT: A 385 MET cc_start: 0.8881 (mmm) cc_final: 0.8449 (mmm) REVERT: B 2 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6744 (tt0) REVERT: B 10 ARG cc_start: 0.2584 (OUTLIER) cc_final: 0.1878 (ptt90) REVERT: B 42 MET cc_start: 0.4282 (mtp) cc_final: 0.3754 (mtp) REVERT: B 114 LYS cc_start: 0.8570 (mmmt) cc_final: 0.8304 (mptt) REVERT: B 171 LYS cc_start: 0.8734 (mttt) cc_final: 0.7973 (tptp) REVERT: C 114 LYS cc_start: 0.8596 (mmmt) cc_final: 0.8373 (mptt) REVERT: C 171 LYS cc_start: 0.8804 (mttt) cc_final: 0.8051 (tptm) REVERT: C 242 LYS cc_start: 0.8190 (ttmm) cc_final: 0.7788 (ttmt) REVERT: C 378 GLN cc_start: 0.7861 (mt0) cc_final: 0.7416 (mm110) REVERT: D 2 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6541 (tt0) REVERT: D 171 LYS cc_start: 0.8778 (mttt) cc_final: 0.8005 (tptp) REVERT: D 242 LYS cc_start: 0.8268 (ttmm) cc_final: 0.8044 (ttmt) REVERT: E 10 ARG cc_start: 0.2537 (OUTLIER) cc_final: 0.1856 (ptt180) REVERT: E 42 MET cc_start: 0.4378 (mtp) cc_final: 0.3904 (mtp) REVERT: E 114 LYS cc_start: 0.8614 (mmmt) cc_final: 0.8336 (mptt) REVERT: E 171 LYS cc_start: 0.8817 (mttt) cc_final: 0.8023 (tptm) REVERT: F 114 LYS cc_start: 0.8555 (mmmt) cc_final: 0.8291 (mptt) REVERT: F 171 LYS cc_start: 0.8861 (mttt) cc_final: 0.8143 (tptp) REVERT: F 378 GLN cc_start: 0.7917 (mt0) cc_final: 0.7459 (mm110) REVERT: G 42 MET cc_start: 0.4427 (mtp) cc_final: 0.4144 (mtp) REVERT: G 57 MET cc_start: 0.6742 (mtm) cc_final: 0.6341 (mtp) REVERT: G 114 LYS cc_start: 0.8508 (mmmt) cc_final: 0.8267 (mptt) REVERT: G 171 LYS cc_start: 0.8851 (mttt) cc_final: 0.8076 (tptp) REVERT: G 254 GLU cc_start: 0.7764 (tt0) cc_final: 0.7521 (tt0) REVERT: G 378 GLN cc_start: 0.7863 (mt0) cc_final: 0.7514 (tp40) outliers start: 21 outliers final: 12 residues processed: 247 average time/residue: 1.2292 time to fit residues: 351.2685 Evaluate side-chains 240 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 225 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain G residue 89 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 56.0241 > 50: distance: 29 - 157: 11.894 distance: 32 - 154: 20.269 distance: 48 - 136: 14.228 distance: 51 - 133: 10.175 distance: 110 - 114: 13.824 distance: 114 - 115: 16.436 distance: 115 - 116: 22.951 distance: 115 - 118: 30.784 distance: 116 - 117: 19.639 distance: 116 - 119: 17.000 distance: 119 - 120: 3.644 distance: 120 - 121: 7.216 distance: 120 - 123: 11.225 distance: 121 - 122: 5.109 distance: 121 - 125: 13.876 distance: 123 - 124: 15.540 distance: 125 - 126: 5.542 distance: 126 - 127: 8.971 distance: 126 - 129: 11.208 distance: 127 - 128: 5.579 distance: 127 - 133: 10.546 distance: 129 - 130: 4.058 distance: 134 - 135: 10.947 distance: 134 - 137: 10.369 distance: 135 - 136: 17.814 distance: 135 - 140: 13.033 distance: 137 - 138: 11.080 distance: 137 - 139: 13.397 distance: 140 - 141: 11.761 distance: 141 - 142: 15.738 distance: 141 - 144: 13.762 distance: 142 - 143: 18.833 distance: 142 - 154: 9.849 distance: 144 - 145: 10.976 distance: 145 - 146: 4.759 distance: 145 - 147: 6.021 distance: 146 - 148: 10.342 distance: 147 - 149: 6.319 distance: 147 - 150: 7.892 distance: 148 - 149: 8.088 distance: 149 - 151: 3.357 distance: 150 - 152: 3.039 distance: 151 - 153: 8.977 distance: 152 - 153: 5.026 distance: 154 - 155: 18.039 distance: 155 - 156: 13.206 distance: 155 - 158: 11.356 distance: 156 - 157: 18.818 distance: 156 - 160: 16.479 distance: 158 - 159: 10.607 distance: 160 - 161: 21.035 distance: 161 - 162: 5.503 distance: 161 - 164: 15.825 distance: 162 - 163: 12.875 distance: 162 - 172: 6.498 distance: 164 - 165: 6.733 distance: 165 - 166: 26.872 distance: 165 - 167: 14.061 distance: 166 - 168: 15.475 distance: 167 - 169: 18.731 distance: 168 - 170: 9.971 distance: 169 - 170: 4.667 distance: 170 - 171: 6.351 distance: 172 - 173: 3.612 distance: 172 - 178: 8.734 distance: 173 - 174: 9.282 distance: 173 - 176: 11.783 distance: 174 - 175: 18.031 distance: 174 - 179: 12.680 distance: 176 - 177: 6.694 distance: 177 - 178: 6.388 distance: 179 - 180: 26.793 distance: 180 - 181: 16.457 distance: 180 - 183: 10.874 distance: 181 - 182: 8.052 distance: 181 - 186: 35.187 distance: 183 - 184: 23.983 distance: 183 - 185: 8.049 distance: 186 - 187: 25.324 distance: 187 - 188: 5.814 distance: 187 - 190: 18.947 distance: 188 - 189: 6.044 distance: 188 - 194: 4.633 distance: 190 - 191: 18.844 distance: 191 - 192: 18.347 distance: 191 - 193: 11.514