Starting phenix.real_space_refine
on Fri Aug 22 14:57:04 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8edo_28038/08_2025/8edo_28038.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8edo_28038/08_2025/8edo_28038.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8edo_28038/08_2025/8edo_28038.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8edo_28038/08_2025/8edo_28038.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8edo_28038/08_2025/8edo_28038.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8edo_28038/08_2025/8edo_28038.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.004
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      11      5.16       5
     C    2828      2.51       5
     N     832      2.21       5
     O     794      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4465
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1984
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 1984
          Classifications: {'peptide': 334}
          Incomplete info: {'truncation_to_alanine': 205}
          Link IDs: {'PTRANS': 9, 'TRANS': 324}
          Chain breaks: 2
          Unresolved chain link angles: 9
          Unresolved non-hydrogen bonds: 589
          Unresolved non-hydrogen angles: 743
          Unresolved non-hydrogen dihedrals: 450
          Unresolved non-hydrogen chiralities: 74
          Planarities with less than four sites: {'ASN:plan1': 16, 'GLU:plan': 16, 'ASP:plan': 18, 'GLN:plan1': 8, 'ARG:plan': 7, 'HIS:plan': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 249
    Chain: "B"
      Number of atoms: 2481
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 417, 2481
          Classifications: {'peptide': 417}
          Incomplete info: {'truncation_to_alanine': 280}
          Link IDs: {'PTRANS': 14, 'TRANS': 402}
          Chain breaks: 3
          Unresolved chain link angles: 14
          Unresolved non-hydrogen bonds: 784
          Unresolved non-hydrogen angles: 998
          Unresolved non-hydrogen dihedrals: 597
          Unresolved non-hydrogen chiralities: 123
          Planarities with less than four sites: {'ASP:plan': 16, 'ARG:plan': 8, 'ASN:plan1': 12, 'GLU:plan': 20, 'HIS:plan': 4, 'PHE:plan': 1, 'GLN:plan1': 8, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 269
  Time building chain proxies: 1.51, per 1000 atoms: 0.34
  Number of scatterers: 4465
  At special positions: 0
  Unit cell: (109.2, 102.96, 83.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      11     16.00
     O     794      8.00
     N     832      7.00
     C    2828      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: 0.54
  Conformation dependent library (CDL) restraints added in 259.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1430

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 0 sheets defined
      81.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1041 through 1049
      removed outlier: 3.693A  pdb=" N   ASP A1047 " --> pdb=" O   GLU A1043 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1058 through 1081
    Processing helix  chain 'A' and resid 1094 through 1116
    Processing helix  chain 'A' and resid 1136 through 1156
      removed outlier: 4.345A  pdb=" N   SER A1140 " --> pdb=" O   ARG A1136 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ARG A1142 " --> pdb=" O   LEU A1138 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ALA A1155 " --> pdb=" O   ASN A1151 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ASN A1156 " --> pdb=" O   LEU A1152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1160 through 1165
      removed outlier: 3.590A  pdb=" N   SER A1164 " --> pdb=" O   GLY A1160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1166 through 1168
      No H-bonds generated for 'chain 'A' and resid 1166 through 1168'
    Processing helix  chain 'A' and resid 1172 through 1188
    Processing helix  chain 'A' and resid 1828 through 1842
      removed outlier: 3.706A  pdb=" N   THR A1832 " --> pdb=" O   ASP A1828 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE A1836 " --> pdb=" O   THR A1832 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   GLY A1842 " --> pdb=" O   LEU A1838 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1845 through 1864
    Processing helix  chain 'A' and resid 1883 through 1898
    Processing helix  chain 'A' and resid 1903 through 1914
      removed outlier: 4.081A  pdb=" N   SER A1914 " --> pdb=" O   ILE A1910 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1917 through 1929
    Processing helix  chain 'A' and resid 1931 through 1937
    Processing helix  chain 'A' and resid 1943 through 1964
    Processing helix  chain 'A' and resid 1967 through 1980
      removed outlier: 4.123A  pdb=" N   GLY A1977 " --> pdb=" O   ALA A1973 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   SER A1978 " --> pdb=" O   LYS A1974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1985 through 2001
    Processing helix  chain 'A' and resid 2004 through 2019
      removed outlier: 3.993A  pdb=" N   VAL A2015 " --> pdb=" O   ALA A2011 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ALA A2016 " --> pdb=" O   ASP A2012 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1164 through 1169
      removed outlier: 3.693A  pdb=" N   LEU B1167 " --> pdb=" O   SER B1164 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLY B1168 " --> pdb=" O   ILE B1165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1828 through 1842
      removed outlier: 4.058A  pdb=" N   ILE B1836 " --> pdb=" O   THR B1832 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   GLY B1842 " --> pdb=" O   LEU B1838 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1883 through 1898
    Processing helix  chain 'B' and resid 1903 through 1916
      removed outlier: 3.863A  pdb=" N   SER B1914 " --> pdb=" O   ILE B1910 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   LYS B1915 " --> pdb=" O   SER B1911 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1917 through 1933
      Proline residue:  B1930  - end of helix
      removed outlier: 4.085A  pdb=" N   SER B1933 " --> pdb=" O   THR B1929 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1934 through 1937
    Processing helix  chain 'B' and resid 1943 through 1964
    Processing helix  chain 'B' and resid 1967 through 1980
      removed outlier: 3.828A  pdb=" N   GLY B1977 " --> pdb=" O   ALA B1973 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   SER B1978 " --> pdb=" O   LYS B1974 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1982 through 1984
      No H-bonds generated for 'chain 'B' and resid 1982 through 1984'
    Processing helix  chain 'B' and resid 1985 through 2001
    Processing helix  chain 'B' and resid 2004 through 2021
      removed outlier: 3.793A  pdb=" N   VAL B2015 " --> pdb=" O   ALA B2011 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   ALA B2016 " --> pdb=" O   ASP B2012 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   GLY B2020 " --> pdb=" O   ALA B2016 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ASN B2021 " --> pdb=" O   LEU B2017 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2021 through 2040
    Processing helix  chain 'B' and resid 2041 through 2043
      No H-bonds generated for 'chain 'B' and resid 2041 through 2043'
    Processing helix  chain 'B' and resid 2047 through 2052
      removed outlier: 6.684A  pdb=" N   LEU B2052 " --> pdb=" O   GLU B2049 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2053 through 2069
      removed outlier: 3.596A  pdb=" N   ARG B2062 " --> pdb=" O   ALA B2058 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   TYR B2063 " --> pdb=" O   ILE B2059 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   MET B2064 " --> pdb=" O   LEU B2060 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   PHE B2069 " --> pdb=" O   LEU B2065 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2070 through 2072
      No H-bonds generated for 'chain 'B' and resid 2070 through 2072'
    Processing helix  chain 'B' and resid 2074 through 2090
      Proline residue:  B2080  - end of helix
    Processing helix  chain 'B' and resid 2094 through 2114
    Processing helix  chain 'B' and resid 2121 through 2135
    Processing helix  chain 'B' and resid 2137 through 2144
      removed outlier: 3.653A  pdb=" N   TYR B2141 " --> pdb=" O   LEU B2137 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU B2142 " --> pdb=" O   PRO B2138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2151 through 2157
      removed outlier: 3.610A  pdb=" N   ILE B2155 " --> pdb=" O   SER B2151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2177 through 2197
    Processing helix  chain 'B' and resid 2203 through 2217
      removed outlier: 3.952A  pdb=" N   PHE B2215 " --> pdb=" O   LEU B2211 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   PHE B2217 " --> pdb=" O   GLN B2213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2222 through 2235
      removed outlier: 4.246A  pdb=" N   ARG B2226 " --> pdb=" O   SER B2222 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   VAL B2229 " --> pdb=" O   PRO B2225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2239 through 2260
    Processing helix  chain 'B' and resid 2262 through 2281
      removed outlier: 3.720A  pdb=" N   SER B2266 " --> pdb=" O   ASP B2262 " (cutoff:3.500A)

    400 hydrogen bonds defined for protein.
    1176 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: 0.74

  Time building geometry restraints manager: 0.67 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 1564
        1.34 -     1.45: 483
        1.45 -     1.57: 2455
        1.57 -     1.69: 0
        1.69 -     1.81: 21
  Bond restraints: 4523
  Sorted by residual:
  bond pdb=" N   GLU A1868 "
       pdb=" CA  GLU A1868 "
    ideal  model  delta    sigma   weight residual
    1.457  1.473 -0.016 1.29e-02 6.01e+03 1.53e+00
  bond pdb=" CG  LEU A1848 "
       pdb=" CD1 LEU A1848 "
    ideal  model  delta    sigma   weight residual
    1.521  1.480  0.041 3.30e-02 9.18e+02 1.51e+00
  bond pdb=" CA  GLU A1868 "
       pdb=" CB  GLU A1868 "
    ideal  model  delta    sigma   weight residual
    1.530  1.549 -0.019 1.69e-02 3.50e+03 1.23e+00
  bond pdb=" CG  LEU A1841 "
       pdb=" CD2 LEU A1841 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.035 3.30e-02 9.18e+02 1.10e+00
  bond pdb=" CB  PHE B2088 "
       pdb=" CG  PHE B2088 "
    ideal  model  delta    sigma   weight residual
    1.502  1.480  0.022 2.30e-02 1.89e+03 8.99e-01
  ... (remaining 4518 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 6090
        1.75 -     3.50: 100
        3.50 -     5.25: 19
        5.25 -     7.00: 3
        7.00 -     8.75: 5
  Bond angle restraints: 6217
  Sorted by residual:
  angle pdb=" N   LYS A1171 "
        pdb=" CA  LYS A1171 "
        pdb=" C   LYS A1171 "
      ideal   model   delta    sigma   weight residual
     114.75  108.04    6.71 1.26e+00 6.30e-01 2.83e+01
  angle pdb=" C   ILE A1867 "
        pdb=" N   GLU A1868 "
        pdb=" CA  GLU A1868 "
      ideal   model   delta    sigma   weight residual
     121.54  129.51   -7.97 1.91e+00 2.74e-01 1.74e+01
  angle pdb=" C   GLU A1926 "
        pdb=" N   TYR A1927 "
        pdb=" CA  TYR A1927 "
      ideal   model   delta    sigma   weight residual
     122.38  115.97    6.41 1.81e+00 3.05e-01 1.25e+01
  angle pdb=" CA  LYS A1171 "
        pdb=" C   LYS A1171 "
        pdb=" N   ASP A1172 "
      ideal   model   delta    sigma   weight residual
     119.80  115.42    4.38 1.34e+00 5.57e-01 1.07e+01
  angle pdb=" N   GLU A1868 "
        pdb=" CA  GLU A1868 "
        pdb=" CB  GLU A1868 "
      ideal   model   delta    sigma   weight residual
     110.49  115.57   -5.08 1.69e+00 3.50e-01 9.04e+00
  ... (remaining 6212 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.14: 2394
       12.14 -    24.29: 116
       24.29 -    36.43: 58
       36.43 -    48.58: 15
       48.58 -    60.72: 5
  Dihedral angle restraints: 2588
    sinusoidal: 401
      harmonic: 2187
  Sorted by residual:
  dihedral pdb=" CA  MET B1967 "
           pdb=" C   MET B1967 "
           pdb=" N   TYR B1968 "
           pdb=" CA  TYR B1968 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -165.02  -14.98     0      5.00e+00 4.00e-02 8.97e+00
  dihedral pdb=" CA  GLY A1160 "
           pdb=" C   GLY A1160 "
           pdb=" N   LEU A1161 "
           pdb=" CA  LEU A1161 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.21  -14.79     0      5.00e+00 4.00e-02 8.75e+00
  dihedral pdb=" CA  GLN A1972 "
           pdb=" CB  GLN A1972 "
           pdb=" CG  GLN A1972 "
           pdb=" CD  GLN A1972 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -106.20   46.20     3      1.50e+01 4.44e-03 8.30e+00
  ... (remaining 2585 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 435
       0.032 -    0.064: 261
       0.064 -    0.096: 63
       0.096 -    0.128: 18
       0.128 -    0.160: 3
  Chirality restraints: 780
  Sorted by residual:
  chirality pdb=" CA  GLU A1868 "
            pdb=" N   GLU A1868 "
            pdb=" C   GLU A1868 "
            pdb=" CB  GLU A1868 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.39e-01
  chirality pdb=" CB  THR A1108 "
            pdb=" CA  THR A1108 "
            pdb=" OG1 THR A1108 "
            pdb=" CG2 THR A1108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.42    0.13 2.00e-01 2.50e+01 4.46e-01
  chirality pdb=" CG  LEU A1856 "
            pdb=" CB  LEU A1856 "
            pdb=" CD1 LEU A1856 "
            pdb=" CD2 LEU A1856 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.72    0.13 2.00e-01 2.50e+01 4.37e-01
  ... (remaining 777 not shown)

  Planarity restraints: 827
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A1103 "   -0.010 2.00e-02 2.50e+03   1.48e-02 3.85e+00
        pdb=" CG  PHE A1103 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE A1103 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE A1103 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE1 PHE A1103 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A1103 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A1103 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A1905 "   -0.011 2.00e-02 2.50e+03   8.64e-03 1.31e+00
        pdb=" CG  PHE A1905 "    0.019 2.00e-02 2.50e+03
        pdb=" CD1 PHE A1905 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE A1905 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A1905 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A1905 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A1905 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B2248 "   -0.080 9.50e-02 1.11e+02   3.61e-02 1.06e+00
        pdb=" NE  ARG B2248 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG B2248 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG B2248 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B2248 "    0.000 2.00e-02 2.50e+03
  ... (remaining 824 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1332
        2.81 -     3.33: 4486
        3.33 -     3.86: 7009
        3.86 -     4.38: 6841
        4.38 -     4.90: 12607
  Nonbonded interactions: 32275
  Sorted by model distance:
  nonbonded pdb=" O   PHE B1913 "
            pdb=" NZ  LYS B1921 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" NH1 ARG A1849 "
            pdb=" O   ILE A1879 "
     model   vdw
     2.391 3.120
  nonbonded pdb=" O   ALA B2216 "
            pdb=" NE2 GLN B2224 "
     model   vdw
     2.414 3.120
  nonbonded pdb=" O   ILE B1918 "
            pdb=" ND1 HIS B1922 "
     model   vdw
     2.424 3.120
  nonbonded pdb=" O   MET A1180 "
            pdb=" OG1 THR A1184 "
     model   vdw
     2.440 3.040
  ... (remaining 32270 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.130
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.190
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
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      :  0.004   0.041   4523  Z= 0.202
  Angle     :  0.612   8.747   6217  Z= 0.342
  Chirality :  0.042   0.160    780
  Planarity :  0.003   0.036    827
  Dihedral  : 11.347  60.719   1158
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.34 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.05 (0.32), residues: 737
  helix:  2.16 (0.23), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.03 (0.48), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B2248 
 TYR   0.013   0.002   TYR A1927 
 PHE   0.034   0.002   PHE A1103 
 TRP   0.010   0.002   TRP B1931 
 HIS   0.005   0.002   HIS B2051 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 4523)
  covalent geometry    : angle       0.61191 ( 6217)
  hydrogen bonds       : bond        0.12922 (  400)
  hydrogen bonds       : angle       4.61880 ( 1176)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.193 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0740
  time to fit residues: 5.6123
Evaluate side-chains
  54 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    0.0020
   chunk 61 optimal weight:    0.0770
   chunk 45 optimal weight:    0.0870
   chunk 27 optimal weight:    5.9990
   overall best weight:    0.2724

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B2267 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.125756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.106392 restraints weight = 11412.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 2.64
r_work: 0.3576 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   4523  Z= 0.090
  Angle     :  0.441   6.758   6217  Z= 0.242
  Chirality :  0.038   0.122    780
  Planarity :  0.002   0.011    827
  Dihedral  :  3.325  15.909    766
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.80 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 10.34 %
    Favored  : 88.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.67 (0.33), residues: 737
  helix:  2.53 (0.22), residues: 552
  sheet:  None (None), residues: 0
  loop : -0.68 (0.49), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1176 
 TYR   0.027   0.002   TYR A1927 
 PHE   0.011   0.001   PHE A1103 
 TRP   0.007   0.001   TRP A1931 
 HIS   0.003   0.001   HIS B2084 

Details of bonding type rmsd
  covalent geometry    : bond        0.00158 ( 4523)
  covalent geometry    : angle       0.44117 ( 6217)
  hydrogen bonds       : bond        0.02997 (  400)
  hydrogen bonds       : angle       3.54677 ( 1176)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A 1041 MET cc_start: 0.5525 (pmm) cc_final: 0.4533 (ttp)
  outliers start: 2
  outliers final: 2
  residues processed: 63
  average time/residue: 0.0629
  time to fit residues: 5.1872
Evaluate side-chains
  57 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1844 SER
Chi-restraints excluded: chain B residue 2205 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 70 optimal weight:   10.0000
   chunk 60 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 56 optimal weight:    0.8980
   chunk 71 optimal weight:    5.9990
   chunk 23 optimal weight:    0.0980
   chunk 3 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A1972 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.123368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.103751 restraints weight = 11348.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 2.71
r_work: 0.3532 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.1516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4523  Z= 0.115
  Angle     :  0.452   5.692   6217  Z= 0.244
  Chirality :  0.038   0.119    780
  Planarity :  0.002   0.017    827
  Dihedral  :  3.278  14.640    766
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.53 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 13.79 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.86 (0.33), residues: 737
  helix:  2.64 (0.23), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.44 (0.49), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B2248 
 TYR   0.020   0.002   TYR A1927 
 PHE   0.017   0.002   PHE A1103 
 TRP   0.005   0.001   TRP B2054 
 HIS   0.003   0.001   HIS B2084 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 4523)
  covalent geometry    : angle       0.45180 ( 6217)
  hydrogen bonds       : bond        0.03249 (  400)
  hydrogen bonds       : angle       3.55084 ( 1176)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.106 
Fit side-chains
REVERT: A 1041 MET cc_start: 0.4937 (pmm) cc_final: 0.4054 (ttp)
REVERT: B 2267 GLN cc_start: 0.8639 (mt0) cc_final: 0.8415 (mt0)
  outliers start: 6
  outliers final: 3
  residues processed: 61
  average time/residue: 0.0693
  time to fit residues: 5.4804
Evaluate side-chains
  54 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1106 TYR
Chi-restraints excluded: chain A residue 1844 SER
Chi-restraints excluded: chain B residue 2205 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 37 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 43 optimal weight:    0.7980
   chunk 59 optimal weight:    9.9990
   chunk 8 optimal weight:   10.0000
   chunk 71 optimal weight:    7.9990
   chunk 31 optimal weight:    9.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    3.1386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.119712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.099815 restraints weight = 11390.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 2.69
r_work: 0.3484 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.1349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   4523  Z= 0.237
  Angle     :  0.613  12.301   6217  Z= 0.324
  Chirality :  0.042   0.155    780
  Planarity :  0.003   0.039    827
  Dihedral  :  4.059  16.954    766
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.02 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 19.54 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.83 (0.32), residues: 737
  helix:  1.95 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.94 (0.46), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B2248 
 TYR   0.017   0.003   TYR A1927 
 PHE   0.018   0.003   PHE A1905 
 TRP   0.008   0.002   TRP B2204 
 HIS   0.006   0.001   HIS B2051 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 4523)
  covalent geometry    : angle       0.61254 ( 6217)
  hydrogen bonds       : bond        0.04481 (  400)
  hydrogen bonds       : angle       4.15278 ( 1176)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A 1041 MET cc_start: 0.5132 (pmm) cc_final: 0.4246 (ttp)
  outliers start: 5
  outliers final: 3
  residues processed: 53
  average time/residue: 0.0673
  time to fit residues: 4.7505
Evaluate side-chains
  55 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1106 TYR
Chi-restraints excluded: chain A residue 1844 SER
Chi-restraints excluded: chain B residue 2205 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 47 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 71 optimal weight:    5.9990
   chunk 26 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9980
   chunk 4 optimal weight:    8.9990
   chunk 42 optimal weight:    9.9990
   chunk 46 optimal weight:    8.9990
   chunk 53 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    2.3184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.120467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.100889 restraints weight = 11396.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 2.54
r_work: 0.3497 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.1456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4523  Z= 0.184
  Angle     :  0.540  11.261   6217  Z= 0.290
  Chirality :  0.040   0.126    780
  Planarity :  0.003   0.028    827
  Dihedral  :  3.896  17.447    766
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.48 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 22.99 %
    Favored  : 74.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.32), residues: 737
  helix:  1.99 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.97 (0.46), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B2248 
 TYR   0.018   0.002   TYR A1927 
 PHE   0.016   0.002   PHE B1905 
 TRP   0.006   0.001   TRP A1976 
 HIS   0.004   0.001   HIS B2084 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 4523)
  covalent geometry    : angle       0.53991 ( 6217)
  hydrogen bonds       : bond        0.03936 (  400)
  hydrogen bonds       : angle       3.91808 ( 1176)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A 1041 MET cc_start: 0.5193 (pmm) cc_final: 0.4370 (ttp)
  outliers start: 5
  outliers final: 3
  residues processed: 58
  average time/residue: 0.0631
  time to fit residues: 4.7907
Evaluate side-chains
  59 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1106 TYR
Chi-restraints excluded: chain A residue 1844 SER
Chi-restraints excluded: chain B residue 2205 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 18 optimal weight:    9.9990
   chunk 70 optimal weight:    5.9990
   chunk 57 optimal weight:    9.9990
   chunk 53 optimal weight:    0.8980
   chunk 71 optimal weight:    9.9990
   chunk 67 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 19 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    2.7586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.119530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.099821 restraints weight = 11634.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 2.56
r_work: 0.3479 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4523  Z= 0.213
  Angle     :  0.582  10.780   6217  Z= 0.309
  Chirality :  0.041   0.188    780
  Planarity :  0.003   0.032    827
  Dihedral  :  4.088  17.729    766
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.16 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 22.41 %
    Favored  : 71.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.52 (0.31), residues: 737
  helix:  1.73 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.05 (0.46), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B2248 
 TYR   0.017   0.003   TYR A1927 
 PHE   0.019   0.002   PHE A1103 
 TRP   0.007   0.002   TRP B1931 
 HIS   0.004   0.001   HIS B2051 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 4523)
  covalent geometry    : angle       0.58217 ( 6217)
  hydrogen bonds       : bond        0.04280 (  400)
  hydrogen bonds       : angle       4.08997 ( 1176)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.178 
Fit side-chains
REVERT: A 1041 MET cc_start: 0.5126 (pmm) cc_final: 0.4254 (ttp)
  outliers start: 10
  outliers final: 6
  residues processed: 63
  average time/residue: 0.0621
  time to fit residues: 5.2441
Evaluate side-chains
  65 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1106 TYR
Chi-restraints excluded: chain A residue 1156 ASN
Chi-restraints excluded: chain A residue 1841 LEU
Chi-restraints excluded: chain B residue 1829 VAL
Chi-restraints excluded: chain B residue 1833 LEU
Chi-restraints excluded: chain B residue 2205 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    0.7980
   chunk 67 optimal weight:    5.9990
   chunk 46 optimal weight:   20.0000
   chunk 68 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   chunk 60 optimal weight:    0.4980
   chunk 29 optimal weight:    0.9980
   overall best weight:    1.2584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.121891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.102533 restraints weight = 11481.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.70
r_work: 0.3511 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.1771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4523  Z= 0.123
  Angle     :  0.502   9.292   6217  Z= 0.264
  Chirality :  0.039   0.138    780
  Planarity :  0.002   0.017    827
  Dihedral  :  3.590  16.929    766
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.34 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 25.29 %
    Favored  : 71.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.32 (0.32), residues: 737
  helix:  2.26 (0.23), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.65 (0.49), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B2248 
 TYR   0.018   0.002   TYR A1927 
 PHE   0.018   0.001   PHE A1103 
 TRP   0.007   0.001   TRP A1976 
 HIS   0.005   0.001   HIS B2084 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 4523)
  covalent geometry    : angle       0.50224 ( 6217)
  hydrogen bonds       : bond        0.03350 (  400)
  hydrogen bonds       : angle       3.65840 ( 1176)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A 1041 MET cc_start: 0.5148 (pmm) cc_final: 0.4303 (ttp)
  outliers start: 5
  outliers final: 2
  residues processed: 58
  average time/residue: 0.0686
  time to fit residues: 5.2574
Evaluate side-chains
  59 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1106 TYR
Chi-restraints excluded: chain B residue 2205 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 17 optimal weight:    0.4980
   chunk 38 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.4784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.121355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.102367 restraints weight = 11590.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 2.46
r_work: 0.3510 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4523  Z= 0.136
  Angle     :  0.522   8.810   6217  Z= 0.274
  Chirality :  0.039   0.152    780
  Planarity :  0.002   0.029    827
  Dihedral  :  3.561  16.068    766
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 23.56 %
    Favored  : 73.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.42 (0.32), residues: 737
  helix:  2.33 (0.23), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.61 (0.49), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B2248 
 TYR   0.018   0.002   TYR A1927 
 PHE   0.021   0.002   PHE B1905 
 TRP   0.006   0.001   TRP A1976 
 HIS   0.004   0.001   HIS B2084 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 4523)
  covalent geometry    : angle       0.52211 ( 6217)
  hydrogen bonds       : bond        0.03461 (  400)
  hydrogen bonds       : angle       3.65591 ( 1176)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A 1041 MET cc_start: 0.5059 (pmm) cc_final: 0.4229 (ttp)
  outliers start: 5
  outliers final: 5
  residues processed: 58
  average time/residue: 0.0712
  time to fit residues: 5.4704
Evaluate side-chains
  60 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1106 TYR
Chi-restraints excluded: chain A residue 1156 ASN
Chi-restraints excluded: chain A residue 1841 LEU
Chi-restraints excluded: chain B residue 1829 VAL
Chi-restraints excluded: chain B residue 2205 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0980
   chunk 41 optimal weight:    0.0870
   chunk 59 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 18 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0870
   chunk 37 optimal weight:    0.9990
   chunk 23 optimal weight:    0.2980
   overall best weight:    0.2536

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B2110 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.125233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.106106 restraints weight = 11399.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 2.58
r_work: 0.3588 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4523  Z= 0.089
  Angle     :  0.467   8.489   6217  Z= 0.244
  Chirality :  0.037   0.154    780
  Planarity :  0.002   0.031    827
  Dihedral  :  3.129  15.859    766
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 24.71 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.90 (0.33), residues: 737
  helix:  2.68 (0.23), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.46 (0.48), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B2248 
 TYR   0.018   0.001   TYR A1927 
 PHE   0.017   0.001   PHE A1103 
 TRP   0.007   0.001   TRP A1976 
 HIS   0.005   0.001   HIS B2084 

Details of bonding type rmsd
  covalent geometry    : bond        0.00169 ( 4523)
  covalent geometry    : angle       0.46716 ( 6217)
  hydrogen bonds       : bond        0.02648 (  400)
  hydrogen bonds       : angle       3.27049 ( 1176)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 59
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A 1041 MET cc_start: 0.4967 (pmm) cc_final: 0.4297 (ttp)
  outliers start: 4
  outliers final: 2
  residues processed: 61
  average time/residue: 0.0624
  time to fit residues: 4.9218
Evaluate side-chains
  56 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1106 TYR
Chi-restraints excluded: chain A residue 1841 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 65 optimal weight:    6.9990
   chunk 48 optimal weight:   10.0000
   chunk 71 optimal weight:    8.9990
   chunk 25 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 50 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    1.5584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.121805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.102900 restraints weight = 11437.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 2.52
r_work: 0.3501 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4523  Z= 0.140
  Angle     :  0.546  11.406   6217  Z= 0.278
  Chirality :  0.040   0.155    780
  Planarity :  0.002   0.020    827
  Dihedral  :  3.425  14.495    766
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 26.44 %
    Favored  : 72.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.83 (0.33), residues: 737
  helix:  2.60 (0.23), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.35 (0.49), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1176 
 TYR   0.017   0.002   TYR A1927 
 PHE   0.016   0.001   PHE A1103 
 TRP   0.006   0.001   TRP A1976 
 HIS   0.003   0.001   HIS B2084 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 4523)
  covalent geometry    : angle       0.54636 ( 6217)
  hydrogen bonds       : bond        0.03375 (  400)
  hydrogen bonds       : angle       3.61001 ( 1176)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A 1041 MET cc_start: 0.4965 (pmm) cc_final: 0.4149 (ttp)
  outliers start: 2
  outliers final: 2
  residues processed: 55
  average time/residue: 0.0629
  time to fit residues: 4.5823
Evaluate side-chains
  55 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1106 TYR
Chi-restraints excluded: chain A residue 1841 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0570
   chunk 35 optimal weight:    0.9980
   chunk 63 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 38 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.7298

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.123202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.104902 restraints weight = 11451.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 2.37
r_work: 0.3540 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4523  Z= 0.100
  Angle     :  0.519  11.419   6217  Z= 0.261
  Chirality :  0.038   0.156    780
  Planarity :  0.002   0.013    827
  Dihedral  :  3.208  15.696    766
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 26.44 %
    Favored  : 71.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.02 (0.33), residues: 737
  helix:  2.70 (0.23), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.17 (0.50), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B2248 
 TYR   0.018   0.001   TYR A1927 
 PHE   0.017   0.001   PHE A1103 
 TRP   0.006   0.001   TRP A1976 
 HIS   0.005   0.001   HIS B2084 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 ( 4523)
  covalent geometry    : angle       0.51945 ( 6217)
  hydrogen bonds       : bond        0.02883 (  400)
  hydrogen bonds       : angle       3.42785 ( 1176)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1066.60 seconds
wall clock time: 18 minutes 47.83 seconds (1127.83 seconds total)