Starting phenix.real_space_refine (version: 1.21rc1) on Sun Oct 8 04:48:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed0_28026/10_2023/8ed0_28026.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed0_28026/10_2023/8ed0_28026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed0_28026/10_2023/8ed0_28026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed0_28026/10_2023/8ed0_28026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed0_28026/10_2023/8ed0_28026.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed0_28026/10_2023/8ed0_28026.pdb" } resolution = 2.72 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= 0.014 sd= 0.236 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 36 5.16 5 C 10242 2.51 5 N 2724 2.21 5 O 3072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 12": "OE1" <-> "OE2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "C GLU 12": "OE1" <-> "OE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "E GLU 12": "OE1" <-> "OE2" Residue "E GLU 67": "OE1" <-> "OE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "F GLU 12": "OE1" <-> "OE2" Residue "F GLU 67": "OE1" <-> "OE2" Residue "F GLU 185": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 16074 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 329} Chain: "B" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 329} Chain: "C" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 329} Chain: "D" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 329} Chain: "E" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 329} Chain: "F" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2679 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 329} Time building chain proxies: 8.70, per 1000 atoms: 0.54 Number of scatterers: 16074 At special positions: 0 Unit cell: (113.1, 123.54, 102.66, 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 36 16.00 O 3072 8.00 N 2724 7.00 C 10242 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.93 Conformation dependent library (CDL) restraints added in 2.5 seconds 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3804 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 8.8% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 2 through 4 No H-bonds generated for 'chain 'A' and resid 2 through 4' Processing helix chain 'A' and resid 77 through 89 Proline residue: A 86 - end of helix Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 273 through 281 Processing helix chain 'B' and resid 2 through 4 No H-bonds generated for 'chain 'B' and resid 2 through 4' Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 77 through 89 Proline residue: B 86 - end of helix Processing helix chain 'B' and resid 190 through 192 No H-bonds generated for 'chain 'B' and resid 190 through 192' Processing helix chain 'B' and resid 273 through 281 Processing helix chain 'C' and resid 2 through 4 No H-bonds generated for 'chain 'C' and resid 2 through 4' Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 77 through 89 Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 190 through 192 No H-bonds generated for 'chain 'C' and resid 190 through 192' Processing helix chain 'C' and resid 273 through 281 Processing helix chain 'D' and resid 2 through 4 No H-bonds generated for 'chain 'D' and resid 2 through 4' Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'D' and resid 77 through 89 Proline residue: D 86 - end of helix Processing helix chain 'D' and resid 190 through 192 No H-bonds generated for 'chain 'D' and resid 190 through 192' Processing helix chain 'D' and resid 273 through 281 Processing helix chain 'E' and resid 2 through 4 No H-bonds generated for 'chain 'E' and resid 2 through 4' Processing helix chain 'E' and resid 57 through 59 No H-bonds generated for 'chain 'E' and resid 57 through 59' Processing helix chain 'E' and resid 77 through 89 Proline residue: E 86 - end of helix Processing helix chain 'E' and resid 190 through 192 No H-bonds generated for 'chain 'E' and resid 190 through 192' Processing helix chain 'E' and resid 273 through 281 Processing helix chain 'F' and resid 2 through 4 No H-bonds generated for 'chain 'F' and resid 2 through 4' Processing helix chain 'F' and resid 57 through 59 No H-bonds generated for 'chain 'F' and resid 57 through 59' Processing helix chain 'F' and resid 77 through 89 Proline residue: F 86 - end of helix Processing helix chain 'F' and resid 190 through 192 No H-bonds generated for 'chain 'F' and resid 190 through 192' Processing helix chain 'F' and resid 273 through 281 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 12 removed outlier: 4.236A pdb=" N LEU A 8 " --> pdb=" O LEU A 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 30 through 31 current: chain 'A' and resid 61 through 75 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 61 through 75 current: chain 'A' and resid 104 through 107 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 104 through 107 current: chain 'A' and resid 128 through 146 removed outlier: 6.405A pdb=" N ASP A 157 " --> pdb=" O ASN A 140 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA A 142 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN A 155 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE A 144 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN A 153 " --> pdb=" O PHE A 144 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 153 through 160 current: chain 'A' and resid 207 through 209 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 207 through 209 current: chain 'A' and resid 243 through 251 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 243 through 251 current: chain 'A' and resid 303 through 315 Processing sheet with id=AA2, first strand: chain 'A' and resid 222 through 223 removed outlier: 3.954A pdb=" N ASP A 238 " --> pdb=" O ASN A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 6 through 12 removed outlier: 4.236A pdb=" N LEU B 8 " --> pdb=" O LEU B 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 30 through 31 current: chain 'B' and resid 61 through 75 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 61 through 75 current: chain 'B' and resid 104 through 107 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 104 through 107 current: chain 'B' and resid 128 through 146 removed outlier: 6.404A pdb=" N ASP B 157 " --> pdb=" O ASN B 140 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA B 142 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN B 155 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE B 144 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN B 153 " --> pdb=" O PHE B 144 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 153 through 160 current: chain 'B' and resid 207 through 209 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 207 through 209 current: chain 'B' and resid 243 through 251 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 243 through 251 current: chain 'B' and resid 303 through 315 Processing sheet with id=AA4, first strand: chain 'B' and resid 222 through 223 removed outlier: 3.954A pdb=" N ASP B 238 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 6 through 12 removed outlier: 4.235A pdb=" N LEU C 8 " --> pdb=" O LEU C 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 30 through 31 current: chain 'C' and resid 61 through 75 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 61 through 75 current: chain 'C' and resid 104 through 107 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 104 through 107 current: chain 'C' and resid 128 through 146 removed outlier: 6.405A pdb=" N ASP C 157 " --> pdb=" O ASN C 140 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA C 142 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN C 155 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE C 144 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN C 153 " --> pdb=" O PHE C 144 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 153 through 160 current: chain 'C' and resid 207 through 209 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 207 through 209 current: chain 'C' and resid 243 through 251 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 243 through 251 current: chain 'C' and resid 303 through 315 Processing sheet with id=AA6, first strand: chain 'C' and resid 222 through 223 removed outlier: 3.954A pdb=" N ASP C 238 " --> pdb=" O ASN C 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 6 through 12 removed outlier: 4.236A pdb=" N LEU D 8 " --> pdb=" O LEU D 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 30 through 31 current: chain 'D' and resid 61 through 75 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 61 through 75 current: chain 'D' and resid 104 through 107 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 104 through 107 current: chain 'D' and resid 128 through 146 removed outlier: 6.405A pdb=" N ASP D 157 " --> pdb=" O ASN D 140 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA D 142 " --> pdb=" O ASN D 155 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN D 155 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE D 144 " --> pdb=" O ASN D 153 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN D 153 " --> pdb=" O PHE D 144 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 153 through 160 current: chain 'D' and resid 207 through 209 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 207 through 209 current: chain 'D' and resid 243 through 251 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 243 through 251 current: chain 'D' and resid 303 through 315 Processing sheet with id=AA8, first strand: chain 'D' and resid 222 through 223 removed outlier: 3.954A pdb=" N ASP D 238 " --> pdb=" O ASN D 223 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 6 through 12 removed outlier: 4.236A pdb=" N LEU E 8 " --> pdb=" O LEU E 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 30 through 31 current: chain 'E' and resid 61 through 75 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 61 through 75 current: chain 'E' and resid 104 through 107 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 104 through 107 current: chain 'E' and resid 128 through 146 removed outlier: 6.405A pdb=" N ASP E 157 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA E 142 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN E 155 " --> pdb=" O ALA E 142 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE E 144 " --> pdb=" O ASN E 153 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN E 153 " --> pdb=" O PHE E 144 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 153 through 160 current: chain 'E' and resid 207 through 209 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 207 through 209 current: chain 'E' and resid 243 through 251 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 243 through 251 current: chain 'E' and resid 303 through 315 Processing sheet with id=AB1, first strand: chain 'E' and resid 222 through 223 removed outlier: 3.953A pdb=" N ASP E 238 " --> pdb=" O ASN E 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 6 through 12 removed outlier: 4.237A pdb=" N LEU F 8 " --> pdb=" O LEU F 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 30 through 31 current: chain 'F' and resid 61 through 75 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 61 through 75 current: chain 'F' and resid 104 through 107 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 104 through 107 current: chain 'F' and resid 128 through 146 removed outlier: 6.405A pdb=" N ASP F 157 " --> pdb=" O ASN F 140 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA F 142 " --> pdb=" O ASN F 155 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN F 155 " --> pdb=" O ALA F 142 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE F 144 " --> pdb=" O ASN F 153 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN F 153 " --> pdb=" O PHE F 144 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 153 through 160 current: chain 'F' and resid 207 through 209 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 207 through 209 current: chain 'F' and resid 243 through 251 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 243 through 251 current: chain 'F' and resid 303 through 315 Processing sheet with id=AB3, first strand: chain 'F' and resid 222 through 223 removed outlier: 3.954A pdb=" N ASP F 238 " --> pdb=" O ASN F 223 " (cutoff:3.500A) 108 hydrogen bonds defined for protein. 324 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.28 Time building geometry restraints manager: 6.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2749 1.31 - 1.43: 4328 1.43 - 1.56: 9279 1.56 - 1.68: 0 1.68 - 1.80: 66 Bond restraints: 16422 Sorted by residual: bond pdb=" CA TYR A 337 " pdb=" C TYR A 337 " ideal model delta sigma weight residual 1.522 1.475 0.047 9.30e-03 1.16e+04 2.58e+01 bond pdb=" CA TYR B 337 " pdb=" C TYR B 337 " ideal model delta sigma weight residual 1.522 1.475 0.047 9.30e-03 1.16e+04 2.55e+01 bond pdb=" CB ASP F 251 " pdb=" CG ASP F 251 " ideal model delta sigma weight residual 1.516 1.412 0.104 2.50e-02 1.60e+03 1.73e+01 bond pdb=" C TYR C 337 " pdb=" O TYR C 337 " ideal model delta sigma weight residual 1.235 1.187 0.048 1.26e-02 6.30e+03 1.48e+01 bond pdb=" CA ASP F 251 " pdb=" C ASP F 251 " ideal model delta sigma weight residual 1.528 1.483 0.044 1.37e-02 5.33e+03 1.04e+01 ... (remaining 16417 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.41: 478 106.41 - 113.30: 8786 113.30 - 120.20: 5681 120.20 - 127.10: 7231 127.10 - 133.99: 150 Bond angle restraints: 22326 Sorted by residual: angle pdb=" N GLU D 338 " pdb=" CA GLU D 338 " pdb=" C GLU D 338 " ideal model delta sigma weight residual 110.97 117.70 -6.73 1.09e+00 8.42e-01 3.82e+01 angle pdb=" N ASP F 251 " pdb=" CA ASP F 251 " pdb=" C ASP F 251 " ideal model delta sigma weight residual 110.53 117.88 -7.35 1.29e+00 6.01e-01 3.24e+01 angle pdb=" N ASP D 251 " pdb=" CA ASP D 251 " pdb=" C ASP D 251 " ideal model delta sigma weight residual 110.41 117.28 -6.87 1.23e+00 6.61e-01 3.12e+01 angle pdb=" N GLU C 338 " pdb=" CA GLU C 338 " pdb=" C GLU C 338 " ideal model delta sigma weight residual 111.11 117.80 -6.69 1.20e+00 6.94e-01 3.11e+01 angle pdb=" N GLU F 338 " pdb=" CA GLU F 338 " pdb=" C GLU F 338 " ideal model delta sigma weight residual 111.03 117.11 -6.08 1.11e+00 8.12e-01 3.00e+01 ... (remaining 22321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 8993 17.80 - 35.60: 505 35.60 - 53.40: 177 53.40 - 71.20: 30 71.20 - 89.00: 27 Dihedral angle restraints: 9732 sinusoidal: 3774 harmonic: 5958 Sorted by residual: dihedral pdb=" CA VAL E 254 " pdb=" C VAL E 254 " pdb=" N LYS E 255 " pdb=" CA LYS E 255 " ideal model delta harmonic sigma weight residual 180.00 159.08 20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" C ARG E 56 " pdb=" N ARG E 56 " pdb=" CA ARG E 56 " pdb=" CB ARG E 56 " ideal model delta harmonic sigma weight residual -122.60 -113.33 -9.27 0 2.50e+00 1.60e-01 1.38e+01 dihedral pdb=" CA PHE F 74 " pdb=" C PHE F 74 " pdb=" N THR F 75 " pdb=" CA THR F 75 " ideal model delta harmonic sigma weight residual 180.00 161.97 18.03 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 9729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2020 0.057 - 0.113: 398 0.113 - 0.170: 87 0.170 - 0.226: 7 0.226 - 0.283: 8 Chirality restraints: 2520 Sorted by residual: chirality pdb=" CA GLU C 338 " pdb=" N GLU C 338 " pdb=" C GLU C 338 " pdb=" CB GLU C 338 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA GLU D 338 " pdb=" N GLU D 338 " pdb=" C GLU D 338 " pdb=" CB GLU D 338 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA TYR B 337 " pdb=" N TYR B 337 " pdb=" C TYR B 337 " pdb=" CB TYR B 337 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2517 not shown) Planarity restraints: 2952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 337 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.49e+00 pdb=" C TYR A 337 " 0.050 2.00e-02 2.50e+03 pdb=" O TYR A 337 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU A 338 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 337 " -0.015 2.00e-02 2.50e+03 2.88e-02 8.29e+00 pdb=" C TYR B 337 " 0.050 2.00e-02 2.50e+03 pdb=" O TYR B 337 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU B 338 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET E 55 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.47e+00 pdb=" C MET E 55 " 0.047 2.00e-02 2.50e+03 pdb=" O MET E 55 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG E 56 " -0.016 2.00e-02 2.50e+03 ... (remaining 2949 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1672 2.74 - 3.28: 15241 3.28 - 3.82: 27269 3.82 - 4.36: 36569 4.36 - 4.90: 59975 Nonbonded interactions: 140726 Sorted by model distance: nonbonded pdb=" NH2 ARG A 132 " pdb=" OE2 GLU C 276 " model vdw 2.201 2.520 nonbonded pdb=" OE2 GLU B 276 " pdb=" NH2 ARG C 132 " model vdw 2.202 2.520 nonbonded pdb=" OE2 GLU D 276 " pdb=" NH2 ARG F 132 " model vdw 2.207 2.520 nonbonded pdb=" NH2 ARG D 132 " pdb=" OE2 GLU E 276 " model vdw 2.212 2.520 nonbonded pdb=" NH2 ARG E 132 " pdb=" OE2 GLU F 276 " model vdw 2.221 2.520 ... (remaining 140721 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.160 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 41.790 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.100 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:11.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 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 : 0.007 0.104 16422 Z= 0.447 Angle : 0.752 9.132 22326 Z= 0.440 Chirality : 0.051 0.283 2520 Planarity : 0.006 0.042 2952 Dihedral : 14.421 89.003 5928 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.90 % Favored : 95.52 % Rotamer: Outliers : 0.18 % Allowed : 13.00 % Favored : 86.82 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.16), residues: 2076 helix: -3.07 (0.33), residues: 126 sheet: -0.77 (0.16), residues: 906 loop : -1.77 (0.15), residues: 1044 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 203 time to evaluate : 1.751 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 205 average time/residue: 1.7291 time to fit residues: 383.7259 Evaluate side-chains 162 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 2.022 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 2.3566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 104 optimal weight: 0.0060 chunk 82 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 110 ASN B 78 ASN ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN D 46 GLN D 110 ASN E 110 ASN F 110 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 16422 Z= 0.301 Angle : 0.552 6.105 22326 Z= 0.284 Chirality : 0.045 0.140 2520 Planarity : 0.005 0.040 2952 Dihedral : 4.765 18.172 2268 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.37 % Allowed : 11.41 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.17), residues: 2076 helix: -2.08 (0.45), residues: 126 sheet: -0.29 (0.16), residues: 912 loop : -1.05 (0.17), residues: 1038 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 176 time to evaluate : 1.726 Fit side-chains outliers start: 57 outliers final: 20 residues processed: 214 average time/residue: 1.5238 time to fit residues: 355.9953 Evaluate side-chains 191 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 171 time to evaluate : 1.799 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 14 residues processed: 6 average time/residue: 0.6546 time to fit residues: 7.1483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 154 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 185 optimal weight: 10.0000 chunk 200 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 148 optimal weight: 0.2980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN B 344 HIS C 78 ASN C 110 ASN C 344 HIS D 344 HIS E 110 ASN F 110 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 16422 Z= 0.172 Angle : 0.470 4.821 22326 Z= 0.239 Chirality : 0.042 0.126 2520 Planarity : 0.004 0.039 2952 Dihedral : 4.264 16.925 2268 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.48 % Allowed : 13.00 % Favored : 84.52 % 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: -0.84 (0.18), residues: 2076 helix: -1.51 (0.48), residues: 126 sheet: -0.15 (0.17), residues: 936 loop : -0.72 (0.18), residues: 1014 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 199 time to evaluate : 1.708 Fit side-chains outliers start: 42 outliers final: 16 residues processed: 224 average time/residue: 1.4903 time to fit residues: 364.8583 Evaluate side-chains 195 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 1.774 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.1610 time to fit residues: 3.6217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 186 optimal weight: 20.0000 chunk 197 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 176 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 overall best weight: 4.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 141 GLN C 110 ASN E 110 ASN F 110 ASN F 270 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 16422 Z= 0.519 Angle : 0.646 7.839 22326 Z= 0.327 Chirality : 0.049 0.165 2520 Planarity : 0.005 0.044 2952 Dihedral : 5.049 19.522 2268 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.49 % Allowed : 12.12 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.18), residues: 2076 helix: -1.40 (0.47), residues: 126 sheet: 0.07 (0.17), residues: 912 loop : -0.69 (0.18), residues: 1038 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 166 time to evaluate : 1.817 Fit side-chains outliers start: 76 outliers final: 38 residues processed: 228 average time/residue: 1.6525 time to fit residues: 410.3562 Evaluate side-chains 199 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 161 time to evaluate : 1.850 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 31 residues processed: 7 average time/residue: 0.6257 time to fit residues: 7.5643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.7980 chunk 111 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 168 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 141 GLN C 78 ASN C 110 ASN D 42 GLN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 GLN F 110 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16422 Z= 0.212 Angle : 0.492 5.335 22326 Z= 0.249 Chirality : 0.043 0.132 2520 Planarity : 0.004 0.038 2952 Dihedral : 4.443 17.636 2268 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.13 % Allowed : 13.30 % Favored : 83.57 % 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: -0.50 (0.18), residues: 2076 helix: -1.05 (0.49), residues: 126 sheet: 0.12 (0.17), residues: 912 loop : -0.57 (0.18), residues: 1038 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 190 time to evaluate : 1.937 Fit side-chains outliers start: 53 outliers final: 29 residues processed: 227 average time/residue: 1.5620 time to fit residues: 386.7362 Evaluate side-chains 203 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 174 time to evaluate : 1.932 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 22 residues processed: 7 average time/residue: 0.4379 time to fit residues: 6.3847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 115 optimal weight: 0.0470 chunk 48 optimal weight: 10.0000 chunk 197 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 91 optimal weight: 0.0000 chunk 16 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 overall best weight: 1.7886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 141 GLN B 42 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 110 ASN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16422 Z= 0.216 Angle : 0.490 5.737 22326 Z= 0.247 Chirality : 0.043 0.133 2520 Planarity : 0.004 0.037 2952 Dihedral : 4.361 17.241 2268 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.61 % Allowed : 13.42 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.18), residues: 2076 helix: -0.85 (0.49), residues: 126 sheet: 0.13 (0.17), residues: 912 loop : -0.50 (0.18), residues: 1038 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 184 time to evaluate : 1.702 Fit side-chains outliers start: 61 outliers final: 34 residues processed: 227 average time/residue: 1.4707 time to fit residues: 365.9797 Evaluate side-chains 209 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 175 time to evaluate : 1.769 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 26 residues processed: 8 average time/residue: 0.2282 time to fit residues: 5.1722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 0.0020 chunk 110 optimal weight: 2.9990 chunk 196 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 141 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 110 ASN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16422 Z= 0.250 Angle : 0.508 5.889 22326 Z= 0.257 Chirality : 0.043 0.138 2520 Planarity : 0.004 0.039 2952 Dihedral : 4.443 17.401 2268 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.13 % Allowed : 14.07 % Favored : 82.80 % 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: -0.40 (0.18), residues: 2076 helix: -0.82 (0.49), residues: 126 sheet: 0.14 (0.17), residues: 912 loop : -0.48 (0.18), residues: 1038 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 175 time to evaluate : 1.956 Fit side-chains outliers start: 53 outliers final: 33 residues processed: 217 average time/residue: 1.4777 time to fit residues: 351.9439 Evaluate side-chains 208 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 175 time to evaluate : 1.828 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 26 residues processed: 7 average time/residue: 0.4371 time to fit residues: 6.3295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 141 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 110 ASN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 16422 Z= 0.440 Angle : 0.603 7.681 22326 Z= 0.304 Chirality : 0.047 0.157 2520 Planarity : 0.005 0.043 2952 Dihedral : 4.915 19.013 2268 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.43 % Allowed : 14.18 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.18), residues: 2076 helix: -0.97 (0.48), residues: 126 sheet: 0.14 (0.17), residues: 912 loop : -0.55 (0.18), residues: 1038 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 164 time to evaluate : 1.709 Fit side-chains outliers start: 58 outliers final: 36 residues processed: 212 average time/residue: 1.5258 time to fit residues: 353.4509 Evaluate side-chains 195 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 159 time to evaluate : 1.876 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 30 residues processed: 7 average time/residue: 0.4401 time to fit residues: 6.5482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 173 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 141 GLN A 344 HIS B 78 ASN C 110 ASN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN F 110 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16422 Z= 0.191 Angle : 0.478 5.072 22326 Z= 0.243 Chirality : 0.042 0.135 2520 Planarity : 0.004 0.037 2952 Dihedral : 4.354 17.009 2268 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.30 % Allowed : 15.25 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.18), residues: 2076 helix: -0.75 (0.50), residues: 126 sheet: 0.15 (0.17), residues: 912 loop : -0.42 (0.18), residues: 1038 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 181 time to evaluate : 1.782 Fit side-chains outliers start: 39 outliers final: 28 residues processed: 213 average time/residue: 1.4623 time to fit residues: 341.3495 Evaluate side-chains 203 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 175 time to evaluate : 1.864 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 26 residues processed: 3 average time/residue: 0.2284 time to fit residues: 3.5568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 203 optimal weight: 9.9990 chunk 187 optimal weight: 0.9980 chunk 161 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 141 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16422 Z= 0.247 Angle : 0.507 5.951 22326 Z= 0.256 Chirality : 0.043 0.140 2520 Planarity : 0.004 0.036 2952 Dihedral : 4.474 17.638 2268 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.13 % Allowed : 15.48 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.18), residues: 2076 helix: -0.70 (0.50), residues: 126 sheet: 0.17 (0.17), residues: 912 loop : -0.41 (0.19), residues: 1038 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 174 time to evaluate : 1.890 Fit side-chains outliers start: 36 outliers final: 28 residues processed: 204 average time/residue: 1.5793 time to fit residues: 353.8781 Evaluate side-chains 200 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 172 time to evaluate : 1.720 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 27 residues processed: 2 average time/residue: 0.2924 time to fit residues: 3.2321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.4714 > 50: distance: 79 - 84: 21.957 distance: 84 - 85: 17.835 distance: 85 - 86: 6.723 distance: 85 - 88: 25.459 distance: 86 - 87: 12.027 distance: 86 - 92: 33.425 distance: 88 - 89: 20.860 distance: 89 - 90: 14.570 distance: 89 - 91: 23.041 distance: 92 - 93: 16.184 distance: 93 - 94: 19.523 distance: 94 - 95: 36.083 distance: 94 - 96: 12.961 distance: 96 - 97: 10.974 distance: 97 - 98: 13.259 distance: 97 - 100: 14.582 distance: 98 - 99: 22.828 distance: 98 - 104: 30.380 distance: 100 - 101: 22.316 distance: 101 - 102: 8.091 distance: 101 - 103: 23.955 distance: 104 - 105: 15.614 distance: 105 - 106: 14.214 distance: 106 - 107: 7.842 distance: 106 - 108: 7.341 distance: 108 - 109: 35.839 distance: 109 - 110: 9.624 distance: 109 - 112: 13.385 distance: 110 - 111: 13.819 distance: 110 - 113: 11.145 distance: 113 - 114: 8.875 distance: 114 - 115: 11.223 distance: 114 - 117: 6.570 distance: 115 - 116: 6.052 distance: 115 - 120: 7.867 distance: 117 - 118: 7.063 distance: 117 - 119: 6.524 distance: 120 - 121: 6.598 distance: 121 - 122: 27.084 distance: 122 - 123: 10.252 distance: 122 - 131: 42.296 distance: 124 - 125: 12.451 distance: 125 - 126: 10.566 distance: 125 - 127: 5.884 distance: 126 - 128: 12.332 distance: 127 - 129: 6.996 distance: 128 - 130: 8.703 distance: 129 - 130: 7.640 distance: 131 - 132: 15.920 distance: 132 - 133: 10.355 distance: 132 - 135: 12.749 distance: 133 - 134: 8.095 distance: 133 - 138: 8.495 distance: 135 - 136: 13.175 distance: 135 - 137: 20.160 distance: 138 - 139: 3.428 distance: 139 - 140: 8.477 distance: 139 - 142: 3.892 distance: 140 - 141: 14.665 distance: 140 - 146: 17.665 distance: 142 - 143: 9.069 distance: 143 - 144: 14.392 distance: 143 - 145: 3.523 distance: 146 - 147: 6.078 distance: 147 - 148: 9.688 distance: 147 - 150: 7.451 distance: 148 - 149: 3.330 distance: 148 - 153: 18.157 distance: 150 - 151: 5.007 distance: 150 - 152: 8.491