Starting phenix.real_space_refine on Sat Jan 18 21:32:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ki6_37252/01_2025/8ki6_37252.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ki6_37252/01_2025/8ki6_37252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ki6_37252/01_2025/8ki6_37252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ki6_37252/01_2025/8ki6_37252.map" model { file = "/net/cci-nas-00/data/ceres_data/8ki6_37252/01_2025/8ki6_37252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ki6_37252/01_2025/8ki6_37252.cif" } resolution = 3.4 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= 0.086 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 90 5.16 5 C 8156 2.51 5 N 2098 2.21 5 O 2407 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 12751 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 12717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1580, 12717 Classifications: {'peptide': 1580} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 44, 'TRANS': 1535} Chain breaks: 11 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'RBV%rna2p': 1, 'RBV%rna3p': 1} Classifications: {'undetermined': 2} Modifications used: {'rna2p': 1, 'rna3p': 1} Link IDs: {'rna3p': 1} Time building chain proxies: 7.37, per 1000 atoms: 0.58 Number of scatterers: 12751 At special positions: 0 Unit cell: (116.63, 125.19, 111.28, 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 90 16.00 O 2407 8.00 N 2098 7.00 C 8156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.6 seconds 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3048 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 6 sheets defined 59.7% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 337 through 345 removed outlier: 3.936A pdb=" N ARG A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 363 Processing helix chain 'A' and resid 364 through 367 Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'A' and resid 397 through 414 removed outlier: 3.532A pdb=" N LEU A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 432 removed outlier: 4.006A pdb=" N LYS A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 455 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.810A pdb=" N GLU A 465 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A 466 " --> pdb=" O LEU A 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 466' Processing helix chain 'A' and resid 491 through 501 Processing helix chain 'A' and resid 521 through 536 Processing helix chain 'A' and resid 591 through 606 Processing helix chain 'A' and resid 664 through 682 Processing helix chain 'A' and resid 690 through 700 removed outlier: 3.566A pdb=" N VAL A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 706 removed outlier: 4.034A pdb=" N CYS A 704 " --> pdb=" O ASN A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 729 Processing helix chain 'A' and resid 730 through 749 Processing helix chain 'A' and resid 797 through 804 Processing helix chain 'A' and resid 828 through 837 Processing helix chain 'A' and resid 837 through 853 Proline residue: A 843 - end of helix Processing helix chain 'A' and resid 853 through 863 Processing helix chain 'A' and resid 874 through 893 removed outlier: 3.627A pdb=" N THR A 893 " --> pdb=" O VAL A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 909 removed outlier: 3.786A pdb=" N MET A 900 " --> pdb=" O LYS A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 927 Processing helix chain 'A' and resid 937 through 954 Processing helix chain 'A' and resid 992 through 1005 removed outlier: 3.758A pdb=" N TYR A 996 " --> pdb=" O LEU A 992 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 997 " --> pdb=" O GLU A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1036 removed outlier: 3.649A pdb=" N VAL A1023 " --> pdb=" O SER A1019 " (cutoff:3.500A) Proline residue: A1024 - end of helix removed outlier: 3.987A pdb=" N PHE A1031 " --> pdb=" O TRP A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1075 Processing helix chain 'A' and resid 1077 through 1089 Processing helix chain 'A' and resid 1094 through 1098 Processing helix chain 'A' and resid 1114 through 1125 Processing helix chain 'A' and resid 1126 through 1130 removed outlier: 3.717A pdb=" N ILE A1130 " --> pdb=" O ILE A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1151 Processing helix chain 'A' and resid 1151 through 1163 removed outlier: 3.878A pdb=" N LEU A1155 " --> pdb=" O GLU A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1180 removed outlier: 3.917A pdb=" N GLY A1180 " --> pdb=" O ILE A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1195 Processing helix chain 'A' and resid 1197 through 1209 removed outlier: 3.966A pdb=" N VAL A1201 " --> pdb=" O HIS A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1235 removed outlier: 3.895A pdb=" N TYR A1228 " --> pdb=" O SER A1224 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP A1229 " --> pdb=" O GLU A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1248 removed outlier: 3.688A pdb=" N VAL A1245 " --> pdb=" O ASP A1241 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET A1246 " --> pdb=" O LEU A1242 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A1248 " --> pdb=" O SER A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1271 Processing helix chain 'A' and resid 1300 through 1319 removed outlier: 4.830A pdb=" N HIS A1316 " --> pdb=" O HIS A1312 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL A1317 " --> pdb=" O THR A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1353 removed outlier: 4.344A pdb=" N ILE A1334 " --> pdb=" O GLY A1330 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG A1335 " --> pdb=" O ASP A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1386 removed outlier: 4.185A pdb=" N LEU A1382 " --> pdb=" O TYR A1378 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A1383 " --> pdb=" O LYS A1379 " (cutoff:3.500A) Processing helix chain 'A' and resid 1393 through 1408 Processing helix chain 'A' and resid 1414 through 1428 Processing helix chain 'A' and resid 1434 through 1439 Processing helix chain 'A' and resid 1459 through 1478 removed outlier: 3.719A pdb=" N SER A1463 " --> pdb=" O ASN A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1514 Processing helix chain 'A' and resid 1517 through 1533 Processing helix chain 'A' and resid 1565 through 1575 removed outlier: 3.693A pdb=" N CYS A1573 " --> pdb=" O LEU A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1598 removed outlier: 3.610A pdb=" N HIS A1591 " --> pdb=" O SER A1587 " (cutoff:3.500A) Processing helix chain 'A' and resid 1601 through 1603 No H-bonds generated for 'chain 'A' and resid 1601 through 1603' Processing helix chain 'A' and resid 1604 through 1620 Processing helix chain 'A' and resid 1630 through 1638 Processing helix chain 'A' and resid 1647 through 1651 Processing helix chain 'A' and resid 1657 through 1664 Processing helix chain 'A' and resid 1667 through 1682 Processing helix chain 'A' and resid 1686 through 1696 removed outlier: 3.624A pdb=" N SER A1696 " --> pdb=" O ASP A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1714 Processing helix chain 'A' and resid 1717 through 1733 Processing helix chain 'A' and resid 1762 through 1769 removed outlier: 3.827A pdb=" N ASN A1765 " --> pdb=" O ILE A1762 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A1767 " --> pdb=" O GLU A1764 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASN A1768 " --> pdb=" O ASN A1765 " (cutoff:3.500A) Processing helix chain 'A' and resid 1770 through 1777 Processing helix chain 'A' and resid 1814 through 1828 Processing helix chain 'A' and resid 1829 through 1835 removed outlier: 4.209A pdb=" N ILE A1833 " --> pdb=" O ASN A1829 " (cutoff:3.500A) Processing helix chain 'A' and resid 1843 through 1850 Processing helix chain 'A' and resid 1891 through 1904 Processing helix chain 'A' and resid 1910 through 1923 Processing helix chain 'A' and resid 1924 through 1936 Proline residue: A1932 - end of helix Processing helix chain 'A' and resid 1958 through 1965 Processing helix chain 'A' and resid 1986 through 2008 Processing helix chain 'A' and resid 2018 through 2030 removed outlier: 4.051A pdb=" N ASN A2030 " --> pdb=" O PHE A2026 " (cutoff:3.500A) Processing helix chain 'A' and resid 2031 through 2043 removed outlier: 4.232A pdb=" N MET A2042 " --> pdb=" O ALA A2038 " (cutoff:3.500A) Processing helix chain 'A' and resid 2052 through 2058 removed outlier: 3.770A pdb=" N ARG A2058 " --> pdb=" O THR A2054 " (cutoff:3.500A) Processing helix chain 'A' and resid 2059 through 2065 removed outlier: 3.680A pdb=" N PHE A2063 " --> pdb=" O LYS A2059 " (cutoff:3.500A) Processing helix chain 'A' and resid 2066 through 2069 Processing sheet with id=AA1, first strand: chain 'A' and resid 508 through 509 removed outlier: 3.682A pdb=" N TYR A 811 " --> pdb=" O ILE A 508 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 810 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 508 through 509 removed outlier: 3.682A pdb=" N TYR A 811 " --> pdb=" O ILE A 508 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 810 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1483 through 1492 removed outlier: 3.899A pdb=" N HIS A1492 " --> pdb=" O ASP A1495 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1411 through 1412 Processing sheet with id=AA5, first strand: chain 'A' and resid 1548 through 1549 Processing sheet with id=AA6, first strand: chain 'A' and resid 1973 through 1975 removed outlier: 3.868A pdb=" N ILE A2084 " --> pdb=" O VAL A1974 " (cutoff:3.500A) 671 hydrogen bonds defined for protein. 1944 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: 4.78 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2096 1.30 - 1.43: 3284 1.43 - 1.56: 7455 1.56 - 1.70: 6 1.70 - 1.83: 147 Bond restraints: 12988 Sorted by residual: bond pdb=" CA PRO A1960 " pdb=" CB PRO A1960 " ideal model delta sigma weight residual 1.533 1.441 0.092 1.42e-02 4.96e+03 4.18e+01 bond pdb=" C VAL A1962 " pdb=" O VAL A1962 " ideal model delta sigma weight residual 1.240 1.168 0.071 1.18e-02 7.18e+03 3.64e+01 bond pdb=" CA PRO A1960 " pdb=" C PRO A1960 " ideal model delta sigma weight residual 1.520 1.448 0.072 1.42e-02 4.96e+03 2.54e+01 bond pdb=" C TRP A1958 " pdb=" O TRP A1958 " ideal model delta sigma weight residual 1.232 1.185 0.048 1.38e-02 5.25e+03 1.19e+01 bond pdb=" CA SER A1965 " pdb=" CB SER A1965 " ideal model delta sigma weight residual 1.530 1.475 0.054 1.58e-02 4.01e+03 1.19e+01 ... (remaining 12983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.44: 17386 5.44 - 10.87: 98 10.87 - 16.31: 13 16.31 - 21.74: 1 21.74 - 27.18: 1 Bond angle restraints: 17499 Sorted by residual: angle pdb=" N PRO A1966 " pdb=" CA PRO A1966 " pdb=" CB PRO A1966 " ideal model delta sigma weight residual 103.25 87.83 15.42 1.05e+00 9.07e-01 2.16e+02 angle pdb=" N PRO A1966 " pdb=" CA PRO A1966 " pdb=" C PRO A1966 " ideal model delta sigma weight residual 112.47 139.65 -27.18 2.06e+00 2.36e-01 1.74e+02 angle pdb=" O LYS A1957 " pdb=" C LYS A1957 " pdb=" N TRP A1958 " ideal model delta sigma weight residual 122.59 135.61 -13.02 1.33e+00 5.65e-01 9.58e+01 angle pdb=" CA LYS A1957 " pdb=" C LYS A1957 " pdb=" N TRP A1958 " ideal model delta sigma weight residual 116.84 100.51 16.33 1.71e+00 3.42e-01 9.12e+01 angle pdb=" N PRO A1960 " pdb=" CA PRO A1960 " pdb=" C PRO A1960 " ideal model delta sigma weight residual 112.47 98.20 14.27 2.06e+00 2.36e-01 4.80e+01 ... (remaining 17494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 6823 17.58 - 35.15: 891 35.15 - 52.73: 201 52.73 - 70.30: 35 70.30 - 87.88: 19 Dihedral angle restraints: 7969 sinusoidal: 3284 harmonic: 4685 Sorted by residual: dihedral pdb=" C TRP A1958 " pdb=" N TRP A1958 " pdb=" CA TRP A1958 " pdb=" CB TRP A1958 " ideal model delta harmonic sigma weight residual -122.60 -106.72 -15.88 0 2.50e+00 1.60e-01 4.03e+01 dihedral pdb=" N TRP A1958 " pdb=" C TRP A1958 " pdb=" CA TRP A1958 " pdb=" CB TRP A1958 " ideal model delta harmonic sigma weight residual 122.80 108.09 14.71 0 2.50e+00 1.60e-01 3.46e+01 dihedral pdb=" CA TYR A2085 " pdb=" C TYR A2085 " pdb=" N SER A2086 " pdb=" CA SER A2086 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 7966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1935 0.131 - 0.261: 52 0.261 - 0.392: 3 0.392 - 0.522: 0 0.522 - 0.653: 1 Chirality restraints: 1991 Sorted by residual: chirality pdb=" CA PRO A1966 " pdb=" N PRO A1966 " pdb=" C PRO A1966 " pdb=" CB PRO A1966 " both_signs ideal model delta sigma weight residual False 2.72 2.07 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CG LEU A 912 " pdb=" CB LEU A 912 " pdb=" CD1 LEU A 912 " pdb=" CD2 LEU A 912 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CG LEU A 677 " pdb=" CB LEU A 677 " pdb=" CD1 LEU A 677 " pdb=" CD2 LEU A 677 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 1988 not shown) Planarity restraints: 2186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A1957 " 0.023 2.00e-02 2.50e+03 5.63e-02 3.17e+01 pdb=" C LYS A1957 " -0.097 2.00e-02 2.50e+03 pdb=" O LYS A1957 " 0.041 2.00e-02 2.50e+03 pdb=" N TRP A1958 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A1958 " 0.025 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C TRP A1958 " -0.087 2.00e-02 2.50e+03 pdb=" O TRP A1958 " 0.032 2.00e-02 2.50e+03 pdb=" N ILE A1959 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1952 " -0.019 2.00e-02 2.50e+03 2.65e-02 1.75e+01 pdb=" CG TRP A1952 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP A1952 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP A1952 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A1952 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A1952 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1952 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1952 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1952 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A1952 " 0.003 2.00e-02 2.50e+03 ... (remaining 2183 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2210 2.77 - 3.30: 11807 3.30 - 3.84: 20431 3.84 - 4.37: 22637 4.37 - 4.90: 40263 Nonbonded interactions: 97348 Sorted by model distance: nonbonded pdb=" O LYS A1440 " pdb=" OG1 THR A1443 " model vdw 2.238 3.040 nonbonded pdb=" O VAL A1997 " pdb=" OG1 THR A2001 " model vdw 2.267 3.040 nonbonded pdb=" O PRO A 512 " pdb=" OG1 THR A 805 " model vdw 2.296 3.040 nonbonded pdb=" OG SER A1372 " pdb=" O TRP A1453 " model vdw 2.299 3.040 nonbonded pdb=" OG SER A1372 " pdb=" OD1 ASN A1452 " model vdw 2.305 3.040 ... (remaining 97343 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 30.460 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 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 : 0.005 0.092 12988 Z= 0.298 Angle : 1.093 27.178 17499 Z= 0.597 Chirality : 0.055 0.653 1991 Planarity : 0.006 0.063 2186 Dihedral : 16.708 87.881 4921 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.13 % Favored : 92.54 % Rotamer: Outliers : 2.06 % Allowed : 16.59 % Favored : 81.35 % Cbeta Deviations : 0.13 % 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: -1.93 (0.19), residues: 1556 helix: -0.59 (0.15), residues: 876 sheet: 0.58 (0.66), residues: 62 loop : -2.46 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP A1952 HIS 0.023 0.001 HIS A1823 PHE 0.046 0.002 PHE A1950 TYR 0.058 0.002 TYR A2085 ARG 0.005 0.001 ARG A2034 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 440 ILE cc_start: 0.7461 (tt) cc_final: 0.7150 (mt) REVERT: A 587 MET cc_start: 0.8249 (ppp) cc_final: 0.8043 (ppp) REVERT: A 822 MET cc_start: 0.8299 (mmm) cc_final: 0.8020 (mmt) REVERT: A 926 ASP cc_start: 0.7214 (t0) cc_final: 0.6962 (m-30) REVERT: A 1034 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7404 (tm-30) REVERT: A 1757 LYS cc_start: 0.5831 (tttm) cc_final: 0.5618 (tttm) outliers start: 30 outliers final: 22 residues processed: 220 average time/residue: 0.2454 time to fit residues: 80.7242 Evaluate side-chains 206 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1247 ASN Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1613 GLN Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1627 VAL Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 2071 ARG Chi-restraints excluded: chain A residue 2076 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 0.9990 chunk 119 optimal weight: 0.0570 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 143 optimal weight: 0.3980 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN A1213 ASN A1578 HIS ** A2040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.177050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.142064 restraints weight = 18062.892| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.74 r_work: 0.3688 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12988 Z= 0.187 Angle : 0.621 9.561 17499 Z= 0.323 Chirality : 0.042 0.192 1991 Planarity : 0.004 0.055 2186 Dihedral : 8.520 78.165 1770 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.04 % Favored : 93.77 % Rotamer: Outliers : 2.41 % Allowed : 16.52 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -0.80 (0.21), residues: 1556 helix: 0.55 (0.17), residues: 889 sheet: 0.43 (0.69), residues: 62 loop : -2.33 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1958 HIS 0.005 0.001 HIS A1235 PHE 0.027 0.001 PHE A1950 TYR 0.017 0.001 TYR A2064 ARG 0.003 0.000 ARG A2034 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 1.411 Fit side-chains REVERT: A 440 ILE cc_start: 0.7603 (tt) cc_final: 0.7115 (mt) REVERT: A 1021 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7644 (tt) REVERT: A 1049 MET cc_start: 0.8301 (mmm) cc_final: 0.8067 (ttt) REVERT: A 1109 GLN cc_start: 0.8243 (pt0) cc_final: 0.7963 (pt0) REVERT: A 1246 MET cc_start: 0.7605 (mmm) cc_final: 0.7395 (mmp) REVERT: A 1635 LYS cc_start: 0.9092 (tttp) cc_final: 0.8828 (ttmt) REVERT: A 1819 MET cc_start: 0.7061 (tpt) cc_final: 0.6598 (tpt) REVERT: A 1823 HIS cc_start: 0.6614 (p-80) cc_final: 0.6133 (p-80) REVERT: A 2006 LEU cc_start: 0.6610 (tt) cc_final: 0.6261 (tp) outliers start: 35 outliers final: 20 residues processed: 215 average time/residue: 0.2328 time to fit residues: 75.5292 Evaluate side-chains 192 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1594 MET Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1961 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 118 optimal weight: 0.1980 chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 117 optimal weight: 0.0870 chunk 126 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 ASN A1602 ASN ** A1613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.175333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.140556 restraints weight = 18110.599| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.73 r_work: 0.3677 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 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 0.034 12988 Z= 0.176 Angle : 0.589 9.949 17499 Z= 0.307 Chirality : 0.042 0.179 1991 Planarity : 0.004 0.049 2186 Dihedral : 7.968 77.348 1748 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.56 % Favored : 93.32 % Rotamer: Outliers : 3.30 % Allowed : 17.48 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -0.37 (0.22), residues: 1556 helix: 0.96 (0.18), residues: 891 sheet: 0.53 (0.70), residues: 61 loop : -2.25 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1958 HIS 0.004 0.001 HIS A1011 PHE 0.036 0.001 PHE A1950 TYR 0.017 0.001 TYR A1911 ARG 0.004 0.000 ARG A1705 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 1.603 Fit side-chains REVERT: A 351 ILE cc_start: 0.7196 (mm) cc_final: 0.6987 (mm) REVERT: A 440 ILE cc_start: 0.7605 (tt) cc_final: 0.7194 (mt) REVERT: A 809 TYR cc_start: 0.7781 (OUTLIER) cc_final: 0.7362 (t80) REVERT: A 1021 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7517 (tt) REVERT: A 1109 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7964 (pt0) REVERT: A 1246 MET cc_start: 0.7500 (mmm) cc_final: 0.7258 (mmt) REVERT: A 1635 LYS cc_start: 0.8960 (tttp) cc_final: 0.8690 (ttmt) REVERT: A 1819 MET cc_start: 0.7086 (tpt) cc_final: 0.6544 (tpt) REVERT: A 1823 HIS cc_start: 0.6769 (p-80) cc_final: 0.6383 (p-80) REVERT: A 1896 MET cc_start: 0.8483 (tpp) cc_final: 0.8215 (tpp) REVERT: A 2006 LEU cc_start: 0.6682 (tt) cc_final: 0.6393 (tp) outliers start: 48 outliers final: 28 residues processed: 215 average time/residue: 0.2348 time to fit residues: 76.0256 Evaluate side-chains 204 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 796 MET Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1272 ASN Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1471 LYS Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1594 MET Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1961 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 21 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 98 optimal weight: 0.0010 chunk 150 optimal weight: 0.0870 chunk 130 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.0570 chunk 90 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 overall best weight: 0.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.177540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.142902 restraints weight = 17981.649| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.73 r_work: 0.3703 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12988 Z= 0.145 Angle : 0.557 9.874 17499 Z= 0.291 Chirality : 0.041 0.180 1991 Planarity : 0.004 0.063 2186 Dihedral : 7.735 76.845 1744 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.11 % Favored : 93.77 % Rotamer: Outliers : 3.30 % Allowed : 18.17 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -0.13 (0.22), residues: 1556 helix: 1.18 (0.18), residues: 895 sheet: 0.60 (0.70), residues: 61 loop : -2.21 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1958 HIS 0.003 0.001 HIS A1235 PHE 0.033 0.001 PHE A1950 TYR 0.013 0.001 TYR A2064 ARG 0.004 0.000 ARG A2034 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 181 time to evaluate : 1.393 Fit side-chains revert: symmetry clash REVERT: A 440 ILE cc_start: 0.7573 (tt) cc_final: 0.7228 (mt) REVERT: A 809 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.7513 (t80) REVERT: A 1021 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7410 (tt) REVERT: A 1109 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8001 (pt0) REVERT: A 1246 MET cc_start: 0.7454 (mmm) cc_final: 0.7241 (mmp) REVERT: A 1398 MET cc_start: 0.7147 (mtp) cc_final: 0.6753 (mtt) REVERT: A 1555 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6869 (mtt90) REVERT: A 1819 MET cc_start: 0.7026 (tpt) cc_final: 0.6499 (tpt) REVERT: A 1823 HIS cc_start: 0.6760 (OUTLIER) cc_final: 0.6398 (p-80) REVERT: A 1872 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7459 (ptp-170) REVERT: A 1896 MET cc_start: 0.8513 (tpp) cc_final: 0.8216 (tpp) REVERT: A 2006 LEU cc_start: 0.6677 (tt) cc_final: 0.6356 (tp) outliers start: 48 outliers final: 29 residues processed: 215 average time/residue: 0.2379 time to fit residues: 75.8564 Evaluate side-chains 211 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 796 MET Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1555 ARG Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1594 MET Chi-restraints excluded: chain A residue 1823 HIS Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1872 ARG Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 2071 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 16 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN A1011 HIS ** A1613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1972 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.167835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.134166 restraints weight = 18299.472| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.75 r_work: 0.3586 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12988 Z= 0.339 Angle : 0.700 15.875 17499 Z= 0.362 Chirality : 0.046 0.191 1991 Planarity : 0.005 0.078 2186 Dihedral : 8.015 76.558 1744 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.26 % Favored : 92.54 % Rotamer: Outliers : 4.89 % Allowed : 17.34 % Favored : 77.77 % 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 (0.22), residues: 1556 helix: 0.97 (0.18), residues: 891 sheet: 0.02 (0.69), residues: 52 loop : -2.23 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1952 HIS 0.008 0.001 HIS A1492 PHE 0.041 0.002 PHE A2061 TYR 0.020 0.002 TYR A 804 ARG 0.002 0.000 ARG A2034 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 178 time to evaluate : 1.421 Fit side-chains revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6128 (OUTLIER) cc_final: 0.5348 (m-10) REVERT: A 369 GLU cc_start: 0.7899 (pp20) cc_final: 0.7430 (pm20) REVERT: A 440 ILE cc_start: 0.7806 (tt) cc_final: 0.7504 (mt) REVERT: A 809 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7601 (t80) REVERT: A 1021 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7416 (tt) REVERT: A 1046 LYS cc_start: 0.5020 (mmtt) cc_final: 0.4590 (mmmt) REVERT: A 1109 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7980 (pp30) REVERT: A 1451 MET cc_start: 0.8785 (mmt) cc_final: 0.8530 (mmm) REVERT: A 1555 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7098 (mtp85) REVERT: A 1819 MET cc_start: 0.6750 (tpt) cc_final: 0.6198 (tpt) REVERT: A 1823 HIS cc_start: 0.6807 (OUTLIER) cc_final: 0.6340 (p-80) REVERT: A 2006 LEU cc_start: 0.6644 (tt) cc_final: 0.6283 (tp) outliers start: 71 outliers final: 42 residues processed: 231 average time/residue: 0.2501 time to fit residues: 85.1862 Evaluate side-chains 216 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1247 ASN Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1471 LYS Chi-restraints excluded: chain A residue 1555 ARG Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1823 HIS Chi-restraints excluded: chain A residue 1831 GLU Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1872 ARG Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 2014 LEU Chi-restraints excluded: chain A residue 2071 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 152 optimal weight: 7.9990 chunk 89 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN A1124 ASN A1349 ASN ** A1613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.172219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.137005 restraints weight = 18302.108| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.72 r_work: 0.3650 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12988 Z= 0.177 Angle : 0.602 13.863 17499 Z= 0.310 Chirality : 0.042 0.178 1991 Planarity : 0.004 0.069 2186 Dihedral : 7.706 76.668 1744 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.98 % Favored : 93.83 % Rotamer: Outliers : 3.03 % Allowed : 18.93 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.22), residues: 1556 helix: 1.19 (0.18), residues: 892 sheet: 0.43 (0.68), residues: 61 loop : -2.25 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1952 HIS 0.020 0.001 HIS A1011 PHE 0.033 0.001 PHE A1950 TYR 0.021 0.001 TYR A1911 ARG 0.003 0.000 ARG A2034 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 1.516 Fit side-chains revert: symmetry clash REVERT: A 440 ILE cc_start: 0.7748 (tt) cc_final: 0.7420 (mt) REVERT: A 809 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.7560 (t80) REVERT: A 1006 MET cc_start: 0.8826 (mmm) cc_final: 0.8342 (mmm) REVERT: A 1021 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7394 (tt) REVERT: A 1109 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8144 (pt0) REVERT: A 1555 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.6746 (mtp85) REVERT: A 1820 GLU cc_start: 0.7770 (tt0) cc_final: 0.6643 (tt0) REVERT: A 1823 HIS cc_start: 0.6852 (OUTLIER) cc_final: 0.6418 (p-80) REVERT: A 2006 LEU cc_start: 0.6638 (tt) cc_final: 0.6359 (tp) outliers start: 44 outliers final: 31 residues processed: 210 average time/residue: 0.2572 time to fit residues: 79.8544 Evaluate side-chains 204 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1124 ASN Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1555 ARG Chi-restraints excluded: chain A residue 1594 MET Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1823 HIS Chi-restraints excluded: chain A residue 1831 GLU Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 2071 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 22 optimal weight: 0.0670 chunk 66 optimal weight: 2.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN A1011 HIS A1124 ASN ** A1613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.172115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.136828 restraints weight = 18158.918| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.72 r_work: 0.3648 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12988 Z= 0.188 Angle : 0.603 13.966 17499 Z= 0.309 Chirality : 0.042 0.179 1991 Planarity : 0.004 0.066 2186 Dihedral : 7.553 76.539 1742 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.17 % Favored : 93.64 % Rotamer: Outliers : 3.51 % Allowed : 18.58 % Favored : 77.91 % 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: -0.10 (0.22), residues: 1556 helix: 1.22 (0.18), residues: 896 sheet: 0.46 (0.69), residues: 61 loop : -2.20 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1952 HIS 0.004 0.001 HIS A1492 PHE 0.040 0.001 PHE A2061 TYR 0.013 0.001 TYR A 923 ARG 0.004 0.000 ARG A2034 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 175 time to evaluate : 1.396 Fit side-chains revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6152 (OUTLIER) cc_final: 0.5358 (m-10) REVERT: A 369 GLU cc_start: 0.7895 (pp20) cc_final: 0.7399 (pm20) REVERT: A 440 ILE cc_start: 0.7743 (tt) cc_final: 0.7410 (mt) REVERT: A 809 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.7599 (t80) REVERT: A 1006 MET cc_start: 0.8822 (mmm) cc_final: 0.8342 (mmm) REVERT: A 1021 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7395 (tt) REVERT: A 1109 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8156 (pt0) REVERT: A 1555 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.6737 (mtp85) REVERT: A 1713 LYS cc_start: 0.7731 (mttp) cc_final: 0.7304 (ttmm) REVERT: A 1820 GLU cc_start: 0.7711 (tt0) cc_final: 0.6719 (tm-30) REVERT: A 1823 HIS cc_start: 0.6839 (OUTLIER) cc_final: 0.6320 (p-80) REVERT: A 2006 LEU cc_start: 0.6653 (tt) cc_final: 0.6325 (tp) outliers start: 51 outliers final: 37 residues processed: 217 average time/residue: 0.2530 time to fit residues: 81.5299 Evaluate side-chains 214 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1124 ASN Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1247 ASN Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1555 ARG Chi-restraints excluded: chain A residue 1594 MET Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1823 HIS Chi-restraints excluded: chain A residue 1831 GLU Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 2071 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 102 optimal weight: 0.8980 chunk 136 optimal weight: 0.0060 chunk 130 optimal weight: 2.9990 chunk 29 optimal weight: 0.0370 chunk 32 optimal weight: 1.9990 chunk 115 optimal weight: 0.0470 chunk 45 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 156 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 overall best weight: 0.2172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN A1124 ASN ** A1613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1978 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.175966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.140986 restraints weight = 18234.590| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.74 r_work: 0.3681 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12988 Z= 0.143 Angle : 0.579 11.182 17499 Z= 0.297 Chirality : 0.041 0.181 1991 Planarity : 0.004 0.059 2186 Dihedral : 7.303 76.549 1742 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.72 % Favored : 94.09 % Rotamer: Outliers : 3.10 % Allowed : 18.93 % Favored : 77.98 % 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: 0.10 (0.22), residues: 1556 helix: 1.38 (0.18), residues: 898 sheet: 0.62 (0.70), residues: 61 loop : -2.15 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1952 HIS 0.031 0.001 HIS A1011 PHE 0.032 0.001 PHE A1950 TYR 0.016 0.001 TYR A 923 ARG 0.004 0.000 ARG A2034 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 1.513 Fit side-chains revert: symmetry clash REVERT: A 369 GLU cc_start: 0.7865 (pp20) cc_final: 0.7374 (pm20) REVERT: A 440 ILE cc_start: 0.7676 (tt) cc_final: 0.7336 (mt) REVERT: A 1006 MET cc_start: 0.8783 (mmm) cc_final: 0.8303 (mmm) REVERT: A 1109 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8055 (pt0) REVERT: A 1398 MET cc_start: 0.7151 (mtp) cc_final: 0.6574 (mtt) REVERT: A 1555 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6972 (mtt90) REVERT: A 1713 LYS cc_start: 0.7638 (mttp) cc_final: 0.7219 (ttmm) REVERT: A 1823 HIS cc_start: 0.6727 (OUTLIER) cc_final: 0.6413 (p-80) REVERT: A 1971 MET cc_start: 0.6427 (tpp) cc_final: 0.6016 (tpp) REVERT: A 2006 LEU cc_start: 0.6652 (tt) cc_final: 0.6381 (tp) outliers start: 45 outliers final: 35 residues processed: 213 average time/residue: 0.2469 time to fit residues: 77.7794 Evaluate side-chains 207 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1124 ASN Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1247 ASN Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1555 ARG Chi-restraints excluded: chain A residue 1594 MET Chi-restraints excluded: chain A residue 1628 ASN Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1823 HIS Chi-restraints excluded: chain A residue 1831 GLU Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 2014 LEU Chi-restraints excluded: chain A residue 2071 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 62 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN A1011 HIS A1124 ASN ** A1613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.171370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.136769 restraints weight = 18186.263| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 3.16 r_work: 0.3601 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12988 Z= 0.238 Angle : 0.634 14.268 17499 Z= 0.325 Chirality : 0.043 0.176 1991 Planarity : 0.004 0.062 2186 Dihedral : 7.332 76.499 1740 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.49 % Favored : 93.32 % Rotamer: Outliers : 3.44 % Allowed : 18.86 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1556 helix: 1.27 (0.18), residues: 898 sheet: 0.46 (0.70), residues: 61 loop : -2.19 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A1952 HIS 0.006 0.001 HIS A1492 PHE 0.045 0.002 PHE A2061 TYR 0.015 0.001 TYR A1465 ARG 0.003 0.000 ARG A2034 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 170 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6202 (OUTLIER) cc_final: 0.5393 (m-10) REVERT: A 369 GLU cc_start: 0.7916 (pp20) cc_final: 0.7417 (pm20) REVERT: A 440 ILE cc_start: 0.7764 (tt) cc_final: 0.7425 (mt) REVERT: A 1006 MET cc_start: 0.8796 (mmm) cc_final: 0.8351 (mmm) REVERT: A 1109 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8188 (pt0) REVERT: A 1555 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6697 (mtp85) REVERT: A 1713 LYS cc_start: 0.7774 (mttp) cc_final: 0.7369 (ttmm) REVERT: A 1823 HIS cc_start: 0.6861 (OUTLIER) cc_final: 0.6363 (p-80) REVERT: A 1971 MET cc_start: 0.6437 (tpp) cc_final: 0.6104 (tpp) REVERT: A 2006 LEU cc_start: 0.6613 (tt) cc_final: 0.6345 (tp) outliers start: 50 outliers final: 37 residues processed: 211 average time/residue: 0.2482 time to fit residues: 77.9379 Evaluate side-chains 206 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1124 ASN Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1247 ASN Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1555 ARG Chi-restraints excluded: chain A residue 1628 ASN Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1823 HIS Chi-restraints excluded: chain A residue 1831 GLU Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 2014 LEU Chi-restraints excluded: chain A residue 2071 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.8497 > 50: distance: 85 - 106: 11.852 distance: 102 - 106: 14.787 distance: 106 - 107: 9.542 distance: 107 - 108: 7.382 distance: 107 - 110: 9.600 distance: 108 - 109: 41.771 distance: 108 - 115: 12.696 distance: 110 - 111: 26.267 distance: 111 - 112: 13.579 distance: 112 - 113: 10.139 distance: 113 - 114: 3.430 distance: 115 - 116: 24.673 distance: 116 - 117: 9.164 distance: 117 - 118: 42.769 distance: 117 - 119: 6.909 distance: 119 - 120: 20.971 distance: 120 - 121: 28.602 distance: 120 - 123: 21.040 distance: 121 - 122: 21.468 distance: 121 - 125: 10.497 distance: 123 - 124: 28.393 distance: 125 - 126: 26.641 distance: 125 - 131: 34.507 distance: 126 - 127: 6.500 distance: 126 - 129: 30.594 distance: 127 - 128: 42.904 distance: 127 - 132: 8.166 distance: 129 - 130: 34.936 distance: 130 - 131: 4.613 distance: 132 - 133: 26.783 distance: 133 - 134: 6.130 distance: 133 - 136: 21.613 distance: 134 - 135: 32.209 distance: 134 - 140: 21.017 distance: 136 - 137: 15.773 distance: 137 - 138: 24.555 distance: 137 - 139: 14.954 distance: 140 - 141: 8.285 distance: 141 - 142: 12.178 distance: 141 - 144: 7.960 distance: 142 - 143: 12.895 distance: 142 - 149: 12.164 distance: 144 - 145: 18.455 distance: 145 - 146: 11.131 distance: 146 - 147: 4.894 distance: 146 - 148: 14.922 distance: 149 - 150: 14.858 distance: 150 - 151: 16.771 distance: 150 - 153: 22.911 distance: 151 - 152: 11.255 distance: 151 - 156: 5.704 distance: 152 - 182: 3.274 distance: 153 - 154: 13.501 distance: 153 - 155: 28.869 distance: 156 - 157: 27.060 distance: 157 - 158: 26.873 distance: 157 - 160: 22.330 distance: 158 - 159: 29.798 distance: 158 - 164: 30.102 distance: 159 - 187: 13.708 distance: 160 - 161: 22.343 distance: 160 - 162: 26.045 distance: 161 - 163: 28.034 distance: 164 - 165: 12.334 distance: 164 - 170: 5.772 distance: 165 - 166: 13.263 distance: 165 - 168: 11.661 distance: 166 - 167: 8.261 distance: 166 - 171: 4.644 distance: 167 - 197: 8.098 distance: 168 - 169: 17.709 distance: 169 - 170: 16.364 distance: 171 - 172: 13.846 distance: 172 - 173: 16.677 distance: 172 - 175: 15.646 distance: 173 - 174: 8.660 distance: 173 - 182: 10.096 distance: 174 - 201: 15.198 distance: 175 - 176: 14.001 distance: 176 - 177: 14.235 distance: 176 - 178: 6.617 distance: 177 - 179: 17.730 distance: 178 - 180: 14.514 distance: 179 - 181: 10.320 distance: 180 - 181: 14.165