Starting phenix.real_space_refine
on Tue Mar  3 19:37:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xp5_33365/03_2026/7xp5_33365.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xp5_33365/03_2026/7xp5_33365.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xp5_33365/03_2026/7xp5_33365.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xp5_33365/03_2026/7xp5_33365.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xp5_33365/03_2026/7xp5_33365.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xp5_33365/03_2026/7xp5_33365.map"
  }
  resolution = 3.08
  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=   0.001 sd=   0.023
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      48      5.16       5
     C    5347      2.51       5
     N    1448      2.21       5
     O    1538      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8381
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 2424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2424
          Classifications: {'peptide': 299}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 8, 'TRANS': 290}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'TRP:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "A"
      Number of atoms: 1960
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1960
          Classifications: {'peptide': 239}
          Link IDs: {'PTRANS': 6, 'TRANS': 232}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
  Time building chain proxies: 1.66, per 1000 atoms: 0.20
  Number of scatterers: 8381
  At special positions: 0
  Unit cell: (82.16, 102.96, 132.08, 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      48     16.00
     O    1538      8.00
     N    1448      7.00
     C    5347      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: 0.70
  Conformation dependent library (CDL) restraints added in 272.3 milliseconds
  

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1998

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 10 sheets defined
      46.1% alpha, 19.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'R' and resid 3 through 39
      removed outlier: 3.697A  pdb=" N   ILE R   7 " --> pdb=" O   THR R   3 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 42 through 71
    Processing helix  chain 'R' and resid 77 through 111
    Processing helix  chain 'R' and resid 115 through 124
    Processing helix  chain 'R' and resid 124 through 155
      Proline residue:  R 136  - end of helix
    Processing helix  chain 'R' and resid 155 through 161
      removed outlier: 3.520A  pdb=" N   GLU R 159 " --> pdb=" O   THR R 155 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 164 through 174
      removed outlier: 4.191A  pdb=" N   TYR R 173 " --> pdb=" O   ARG R 169 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 176 through 213
      removed outlier: 4.372A  pdb=" N   VAL R 186 " --> pdb=" O   LEU R 182 " (cutoff:3.500A)
      Proline residue:  R 187  - end of helix
      removed outlier: 3.773A  pdb=" N   HIS R 212 " --> pdb=" O   LYS R 208 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 218 through 255
      removed outlier: 4.790A  pdb=" N   PHE R 252 " --> pdb=" O   SER R 248 " (cutoff:3.500A)
      removed outlier: 5.259A  pdb=" N   GLU R 253 " --> pdb=" O   VAL R 249 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   SER R 254 " --> pdb=" O   TRP R 250 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 257 through 283
      Proline residue:  R 272  - end of helix
      Proline residue:  R 276  - end of helix
    Processing helix  chain 'R' and resid 283 through 301
    Processing helix  chain 'A' and resid 6 through 35
    Processing helix  chain 'A' and resid 48 through 60
    Processing helix  chain 'A' and resid 98 through 104
      removed outlier: 3.934A  pdb=" N   ASN A 104 " --> pdb=" O   GLN A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 134
    Processing helix  chain 'A' and resid 148 through 159
    Processing helix  chain 'A' and resid 162 through 167
      removed outlier: 4.076A  pdb=" N   TYR A 166 " --> pdb=" O   LYS A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 172
      removed outlier: 3.618A  pdb=" N   ALA A 171 " --> pdb=" O   PRO A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 205
      removed outlier: 4.184A  pdb=" N   THR A 190 " --> pdb=" O   ASP A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 247
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.704A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 4.193A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'N' and resid 62 through 65
      removed outlier: 3.513A  pdb=" N   LYS N  65 " --> pdb=" O   GLY N  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 62 through 65'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 79
      removed outlier: 4.753A  pdb=" N   VAL A  89 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 7.673A  pdb=" N   GLY A  43 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   VAL A 142 " --> pdb=" O   TYR A 215 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   HIS A 217 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   LEU A 144 " --> pdb=" O   HIS A 217 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.691A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.697A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.106A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.192A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.818A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.064A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.543A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.458A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.951A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 6.554A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    484 hydrogen bonds defined for protein.
    1407 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: 1.16

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2716
        1.34 -     1.46: 2030
        1.46 -     1.58: 3744
        1.58 -     1.70: 0
        1.70 -     1.81: 68
  Bond restraints: 8558
  Sorted by residual:
  bond pdb=" CG  LEU A 144 "
       pdb=" CD2 LEU A 144 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.18e+00
  bond pdb=" CB  GLN B  75 "
       pdb=" CG  GLN B  75 "
    ideal  model  delta    sigma   weight residual
    1.520  1.489  0.031 3.00e-02 1.11e+03 1.09e+00
  bond pdb=" CA  ARG B  52 "
       pdb=" CB  ARG B  52 "
    ideal  model  delta    sigma   weight residual
    1.526  1.541 -0.015 1.70e-02 3.46e+03 8.08e-01
  bond pdb=" C   GLY N   8 "
       pdb=" N   GLY N   9 "
    ideal  model  delta    sigma   weight residual
    1.331  1.318  0.012 1.46e-02 4.69e+03 7.14e-01
  bond pdb=" C   LYS A  24 "
       pdb=" O   LYS A  24 "
    ideal  model  delta    sigma   weight residual
    1.236  1.246 -0.010 1.15e-02 7.56e+03 7.05e-01
  ... (remaining 8553 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 11290
        1.54 -     3.07: 247
        3.07 -     4.61: 43
        4.61 -     6.15: 9
        6.15 -     7.69: 5
  Bond angle restraints: 11594
  Sorted by residual:
  angle pdb=" C   ILE B  58 "
        pdb=" N   TYR B  59 "
        pdb=" CA  TYR B  59 "
      ideal   model   delta    sigma   weight residual
     122.42  116.39    6.03 1.55e+00 4.16e-01 1.51e+01
  angle pdb=" CA  ARG A  16 "
        pdb=" CB  ARG A  16 "
        pdb=" CG  ARG A  16 "
      ideal   model   delta    sigma   weight residual
     114.10  121.79   -7.69 2.00e+00 2.50e-01 1.48e+01
  angle pdb=" CB  ARG A  16 "
        pdb=" CG  ARG A  16 "
        pdb=" CD  ARG A  16 "
      ideal   model   delta    sigma   weight residual
     111.30  118.01   -6.71 2.30e+00 1.89e-01 8.52e+00
  angle pdb=" CA  GLU G  17 "
        pdb=" CB  GLU G  17 "
        pdb=" CG  GLU G  17 "
      ideal   model   delta    sigma   weight residual
     114.10  119.58   -5.48 2.00e+00 2.50e-01 7.50e+00
  angle pdb=" C   ASP A 223 "
        pdb=" CA  ASP A 223 "
        pdb=" CB  ASP A 223 "
      ideal   model   delta    sigma   weight residual
     110.42  115.85   -5.43 1.99e+00 2.53e-01 7.45e+00
  ... (remaining 11589 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 4678
       17.95 -    35.90: 336
       35.90 -    53.85: 58
       53.85 -    71.80: 3
       71.80 -    89.75: 4
  Dihedral angle restraints: 5079
    sinusoidal: 1998
      harmonic: 3081
  Sorted by residual:
  dihedral pdb=" CA  GLY B 185 "
           pdb=" C   GLY B 185 "
           pdb=" N   ASP B 186 "
           pdb=" CA  ASP B 186 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.85   21.15     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CA  LYS G  20 "
           pdb=" C   LYS G  20 "
           pdb=" N   MET G  21 "
           pdb=" CA  MET G  21 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.09   19.91     0      5.00e+00 4.00e-02 1.58e+01
  dihedral pdb=" CA  VAL A 222 "
           pdb=" C   VAL A 222 "
           pdb=" N   ASP A 223 "
           pdb=" CA  ASP A 223 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.05   18.95     0      5.00e+00 4.00e-02 1.44e+01
  ... (remaining 5076 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 959
       0.045 -    0.090: 280
       0.090 -    0.135: 72
       0.135 -    0.180: 4
       0.180 -    0.225: 2
  Chirality restraints: 1317
  Sorted by residual:
  chirality pdb=" CA  TYR B  59 "
            pdb=" N   TYR B  59 "
            pdb=" C   TYR B  59 "
            pdb=" CB  TYR B  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CB  THR B 181 "
            pdb=" CA  THR B 181 "
            pdb=" OG1 THR B 181 "
            pdb=" CG2 THR B 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.18 2.00e-01 2.50e+01 8.35e-01
  chirality pdb=" CB  VAL N 110 "
            pdb=" CA  VAL N 110 "
            pdb=" CG1 VAL N 110 "
            pdb=" CG2 VAL N 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.32e-01
  ... (remaining 1314 not shown)

  Planarity restraints: 1466
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "    0.027 2.00e-02 2.50e+03   2.13e-02 9.09e+00
        pdb=" CG  TYR B  59 "   -0.052 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "   -0.036 5.00e-02 4.00e+02   5.40e-02 4.67e+00
        pdb=" N   PRO G  49 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 135 "   -0.031 5.00e-02 4.00e+02   4.67e-02 3.48e+00
        pdb=" N   PRO R 136 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO R 136 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO R 136 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1463 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 710
        2.74 -     3.28: 8541
        3.28 -     3.82: 14077
        3.82 -     4.36: 16094
        4.36 -     4.90: 28353
  Nonbonded interactions: 67775
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OG1 THR B  86 "
            pdb=" OD1 ASN B  88 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   ASP B 163 "
            pdb=" OG1 THR B 164 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" ND2 ASN N  35 "
            pdb=" OD2 ASP N 109 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" N   THR B 184 "
            pdb=" OD2 ASP B 205 "
     model   vdw
     2.277 3.120
  ... (remaining 67770 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:             1.000
  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:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.390
  Find NCS groups from input model:        0.040
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
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   0.036   8558  Z= 0.175
  Angle     :  0.593   7.687  11594  Z= 0.322
  Chirality :  0.043   0.225   1317
  Planarity :  0.004   0.054   1466
  Dihedral  : 12.659  89.748   3081
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  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 are not related in a simple way.
  whole:  1.69 (0.26), residues: 1047
  helix:  2.69 (0.23), residues: 441
  sheet:  0.79 (0.34), residues: 221
  loop : -0.58 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A  16 
 TYR   0.052   0.002   TYR B  59 
 PHE   0.019   0.001   PHE A 195 
 TRP   0.022   0.002   TRP B 339 
 HIS   0.004   0.001   HIS R 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 8558)
  covalent geometry    : angle       0.59267 (11594)
  hydrogen bonds       : bond        0.11376 (  484)
  hydrogen bonds       : angle       5.28496 ( 1407)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 281
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: R   22 PHE cc_start: 0.7175 (t80) cc_final: 0.6957 (t80)
REVERT: R  162 MET cc_start: 0.4347 (ptt) cc_final: 0.4093 (ptt)
REVERT: R  207 LYS cc_start: 0.7918 (ttpt) cc_final: 0.7635 (ttpt)
REVERT: R  285 LYS cc_start: 0.8232 (tmtt) cc_final: 0.7940 (tmtt)
REVERT: A  123 GLU cc_start: 0.7019 (tt0) cc_final: 0.6742 (tt0)
REVERT: A  236 ASP cc_start: 0.7567 (t70) cc_final: 0.7218 (t0)
REVERT: B   49 ARG cc_start: 0.6929 (mpt90) cc_final: 0.6616 (mpt90)
REVERT: B   76 ASP cc_start: 0.7267 (p0) cc_final: 0.6933 (p0)
REVERT: B  314 ARG cc_start: 0.7758 (ptm160) cc_final: 0.7446 (ttt180)
REVERT: G   38 MET cc_start: 0.5923 (ppp) cc_final: 0.5517 (ppp)
REVERT: N   80 TYR cc_start: 0.7505 (m-80) cc_final: 0.7248 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 281
  average time/residue: 0.1076
  time to fit residues: 38.8903
Evaluate side-chains
  265 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 265
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0770
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.3980
   chunk 100 optimal weight:    0.0270
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
R  21 ASN
** R 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  78 GLN
B  88 ASN
B  91 HIS
B 340 ASN
G  59 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.144383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.124921 restraints weight = 12543.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3643 rms_B_bonded: 2.37
r_work: 0.3509 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.1004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8558  Z= 0.139
  Angle     :  0.537   6.652  11594  Z= 0.292
  Chirality :  0.042   0.149   1317
  Planarity :  0.004   0.051   1466
  Dihedral  :  4.450  19.495   1139
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 12.23 %
    Favored  : 86.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.73 (0.26), residues: 1047
  helix:  2.81 (0.23), residues: 442
  sheet:  1.00 (0.35), residues: 212
  loop : -0.76 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  68 
 TYR   0.029   0.002   TYR B  59 
 PHE   0.023   0.001   PHE A  77 
 TRP   0.014   0.001   TRP R  97 
 HIS   0.005   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8558)
  covalent geometry    : angle       0.53738 (11594)
  hydrogen bonds       : bond        0.04632 (  484)
  hydrogen bonds       : angle       4.41301 ( 1407)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 274
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
REVERT: R   22 PHE cc_start: 0.7618 (t80) cc_final: 0.7337 (t80)
REVERT: R   24 ASN cc_start: 0.7853 (m-40) cc_final: 0.7620 (m-40)
REVERT: R  122 LYS cc_start: 0.7911 (tttp) cc_final: 0.7671 (tttp)
REVERT: R  162 MET cc_start: 0.4404 (ptt) cc_final: 0.4060 (ptt)
REVERT: R  191 THR cc_start: 0.8265 (t) cc_final: 0.8048 (p)
REVERT: R  207 LYS cc_start: 0.8222 (ttpt) cc_final: 0.7973 (ttpt)
REVERT: R  209 MET cc_start: 0.7939 (mmm) cc_final: 0.7640 (mmm)
REVERT: R  285 LYS cc_start: 0.8504 (tmtt) cc_final: 0.8097 (tmtt)
REVERT: A   56 MET cc_start: 0.6843 (tpt) cc_final: 0.6589 (tpt)
REVERT: A   59 LEU cc_start: 0.8375 (mp) cc_final: 0.8026 (mp)
REVERT: A  123 GLU cc_start: 0.7665 (tt0) cc_final: 0.7301 (tt0)
REVERT: A  128 PHE cc_start: 0.8479 (t80) cc_final: 0.8169 (t80)
REVERT: A  146 LEU cc_start: 0.7715 (mt) cc_final: 0.7419 (mp)
REVERT: A  188 ARG cc_start: 0.7852 (mtm-85) cc_final: 0.7614 (mtm-85)
REVERT: A  197 ARG cc_start: 0.8609 (ttp80) cc_final: 0.8349 (ttp-170)
REVERT: A  202 ARG cc_start: 0.7747 (mtm180) cc_final: 0.7364 (mtm180)
REVERT: A  228 LYS cc_start: 0.7526 (tptm) cc_final: 0.7320 (mmmm)
REVERT: A  236 ASP cc_start: 0.8310 (t70) cc_final: 0.7885 (t0)
REVERT: B   38 ASP cc_start: 0.7746 (m-30) cc_final: 0.7520 (m-30)
REVERT: B   49 ARG cc_start: 0.7589 (mpt90) cc_final: 0.7305 (mpt90)
REVERT: B  186 ASP cc_start: 0.7526 (m-30) cc_final: 0.7281 (m-30)
REVERT: B  190 LEU cc_start: 0.8708 (pp) cc_final: 0.8500 (pp)
REVERT: B  214 ARG cc_start: 0.8369 (mtt-85) cc_final: 0.8098 (ttm110)
REVERT: B  256 ARG cc_start: 0.8347 (mtm110) cc_final: 0.7968 (ptp-110)
REVERT: B  314 ARG cc_start: 0.7974 (ptm160) cc_final: 0.7663 (ttt180)
REVERT: G   38 MET cc_start: 0.6649 (ppp) cc_final: 0.6080 (ppp)
REVERT: N   80 TYR cc_start: 0.7775 (m-80) cc_final: 0.7482 (m-80)
REVERT: N  117 TYR cc_start: 0.8341 (m-80) cc_final: 0.8069 (m-80)
  outliers start: 11
  outliers final: 9
  residues processed: 276
  average time/residue: 0.1087
  time to fit residues: 38.6762
Evaluate side-chains
  277 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 268
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   21 ASN
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue  193 ILE
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain N residue   59 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 99 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0370
   chunk 39 optimal weight:    0.9990
   chunk 100 optimal weight:    0.0170
   chunk 42 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.3896

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

Flipped N/Q/H residues before XYZ refinement:
R  21 ASN
R 143 HIS
A   8 GLN
A  78 GLN
B 239 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.145010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.125828 restraints weight = 12525.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 2.36
r_work: 0.3521 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.1319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8558  Z= 0.120
  Angle     :  0.493   5.046  11594  Z= 0.268
  Chirality :  0.040   0.144   1317
  Planarity :  0.004   0.046   1466
  Dihedral  :  4.280  18.129   1139
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.08 %
    Favored  : 83.84 %
  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 are not related in a simple way.
  whole:  1.79 (0.26), residues: 1047
  helix:  2.91 (0.23), residues: 442
  sheet:  1.06 (0.35), residues: 209
  loop : -0.81 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  68 
 TYR   0.021   0.001   TYR B  59 
 PHE   0.019   0.001   PHE A  77 
 TRP   0.015   0.001   TRP R  97 
 HIS   0.004   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 8558)
  covalent geometry    : angle       0.49296 (11594)
  hydrogen bonds       : bond        0.04216 (  484)
  hydrogen bonds       : angle       4.22810 ( 1407)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 280
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   22 PHE cc_start: 0.7591 (t80) cc_final: 0.7304 (t80)
REVERT: R   24 ASN cc_start: 0.7758 (m-40) cc_final: 0.7323 (m110)
REVERT: R  122 LYS cc_start: 0.7856 (tttp) cc_final: 0.7554 (tttp)
REVERT: R  162 MET cc_start: 0.4392 (ptt) cc_final: 0.4028 (ptt)
REVERT: R  191 THR cc_start: 0.8207 (t) cc_final: 0.7948 (p)
REVERT: R  207 LYS cc_start: 0.8241 (ttpt) cc_final: 0.7987 (ttpt)
REVERT: R  285 LYS cc_start: 0.8481 (tmtt) cc_final: 0.8046 (tmtt)
REVERT: A   56 MET cc_start: 0.6831 (tpt) cc_final: 0.6619 (tpt)
REVERT: A  121 LEU cc_start: 0.7779 (tp) cc_final: 0.7466 (mt)
REVERT: A  123 GLU cc_start: 0.7688 (tt0) cc_final: 0.7326 (tt0)
REVERT: A  128 PHE cc_start: 0.8460 (t80) cc_final: 0.8191 (t80)
REVERT: A  188 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7569 (mtm-85)
REVERT: A  195 PHE cc_start: 0.8162 (t80) cc_final: 0.7824 (t80)
REVERT: A  202 ARG cc_start: 0.7759 (mtm180) cc_final: 0.7231 (mtm180)
REVERT: A  228 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7280 (mmmm)
REVERT: A  232 ASP cc_start: 0.7399 (m-30) cc_final: 0.7167 (m-30)
REVERT: A  236 ASP cc_start: 0.8363 (t70) cc_final: 0.7941 (t0)
REVERT: B   22 ARG cc_start: 0.7228 (mtt180) cc_final: 0.6630 (mtt180)
REVERT: B   25 CYS cc_start: 0.7852 (m) cc_final: 0.7452 (m)
REVERT: B   38 ASP cc_start: 0.7712 (m-30) cc_final: 0.7490 (m-30)
REVERT: B   49 ARG cc_start: 0.7637 (mpt90) cc_final: 0.7295 (mpt90)
REVERT: B   68 ARG cc_start: 0.8318 (ttt-90) cc_final: 0.8069 (ttt-90)
REVERT: B  186 ASP cc_start: 0.7433 (m-30) cc_final: 0.7182 (m-30)
REVERT: B  190 LEU cc_start: 0.8688 (pp) cc_final: 0.8455 (pp)
REVERT: B  214 ARG cc_start: 0.8378 (mtt-85) cc_final: 0.8110 (ttm110)
REVERT: B  314 ARG cc_start: 0.7981 (ptm160) cc_final: 0.7711 (ttt180)
REVERT: G   38 MET cc_start: 0.6666 (ppp) cc_final: 0.6076 (ppp)
REVERT: N   80 TYR cc_start: 0.7751 (m-80) cc_final: 0.7490 (m-80)
  outliers start: 19
  outliers final: 16
  residues processed: 284
  average time/residue: 0.1102
  time to fit residues: 40.3400
Evaluate side-chains
  285 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 268
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue  143 HIS
Chi-restraints excluded: chain R residue  221 MET
Chi-restraints excluded: chain R residue  297 VAL
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  228 LYS
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue  111 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   chunk 88 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 95 optimal weight:    0.3980
   chunk 13 optimal weight:    0.0070
   chunk 9 optimal weight:    0.5980
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
R  21 ASN
R 143 HIS
R 176 ASN
A  78 GLN
B  91 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.144631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.125607 restraints weight = 12695.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 2.38
r_work: 0.3514 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8558  Z= 0.123
  Angle     :  0.489   5.386  11594  Z= 0.264
  Chirality :  0.040   0.144   1317
  Planarity :  0.004   0.046   1466
  Dihedral  :  4.223  17.935   1139
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 16.70 %
    Favored  : 81.11 %
  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 are not related in a simple way.
  whole:  1.82 (0.26), residues: 1047
  helix:  2.96 (0.23), residues: 442
  sheet:  1.04 (0.34), residues: 210
  loop : -0.82 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 219 
 TYR   0.016   0.001   TYR B  59 
 PHE   0.019   0.001   PHE A  77 
 TRP   0.014   0.001   TRP R  97 
 HIS   0.006   0.001   HIS R 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8558)
  covalent geometry    : angle       0.48949 (11594)
  hydrogen bonds       : bond        0.04134 (  484)
  hydrogen bonds       : angle       4.15472 ( 1407)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 274
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   22 PHE cc_start: 0.7626 (t80) cc_final: 0.7329 (t80)
REVERT: R  162 MET cc_start: 0.4447 (ptt) cc_final: 0.4101 (ptt)
REVERT: R  207 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7968 (ttpt)
REVERT: R  285 LYS cc_start: 0.8480 (tmtt) cc_final: 0.8074 (tmtt)
REVERT: A   56 MET cc_start: 0.6827 (tpt) cc_final: 0.6601 (tpt)
REVERT: A  121 LEU cc_start: 0.7782 (tp) cc_final: 0.7479 (mt)
REVERT: A  123 GLU cc_start: 0.7675 (tt0) cc_final: 0.7302 (tt0)
REVERT: A  128 PHE cc_start: 0.8460 (t80) cc_final: 0.8231 (t80)
REVERT: A  195 PHE cc_start: 0.8155 (t80) cc_final: 0.7779 (t80)
REVERT: A  202 ARG cc_start: 0.7707 (mtm180) cc_final: 0.7109 (mtm180)
REVERT: A  228 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7241 (mmmm)
REVERT: A  236 ASP cc_start: 0.8360 (t70) cc_final: 0.7967 (t0)
REVERT: B   22 ARG cc_start: 0.7263 (mtt180) cc_final: 0.6542 (mtt180)
REVERT: B   25 CYS cc_start: 0.7843 (m) cc_final: 0.7452 (m)
REVERT: B   38 ASP cc_start: 0.7691 (m-30) cc_final: 0.7437 (m-30)
REVERT: B   49 ARG cc_start: 0.7648 (mpt90) cc_final: 0.7340 (mpt90)
REVERT: B   68 ARG cc_start: 0.8379 (ttt-90) cc_final: 0.7969 (ttp80)
REVERT: B  186 ASP cc_start: 0.7470 (m-30) cc_final: 0.7229 (m-30)
REVERT: B  190 LEU cc_start: 0.8684 (pp) cc_final: 0.8448 (pp)
REVERT: B  214 ARG cc_start: 0.8359 (mtt-85) cc_final: 0.8151 (ttm110)
REVERT: B  258 ASP cc_start: 0.8135 (t70) cc_final: 0.6539 (t70)
REVERT: B  314 ARG cc_start: 0.7974 (ptm160) cc_final: 0.7764 (ttt180)
REVERT: G   25 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7719 (mp)
REVERT: G   38 MET cc_start: 0.6662 (ppp) cc_final: 0.6082 (ppp)
REVERT: N   80 TYR cc_start: 0.7747 (m-80) cc_final: 0.7453 (m-80)
  outliers start: 20
  outliers final: 15
  residues processed: 279
  average time/residue: 0.1114
  time to fit residues: 39.8446
Evaluate side-chains
  285 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 268
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   21 ASN
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue  221 MET
Chi-restraints excluded: chain R residue  297 VAL
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  228 LYS
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue  111 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 5 optimal weight:    0.1980
   chunk 91 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 73 optimal weight:    0.3980
   chunk 12 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** R  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 143 HIS
R 176 ASN
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
N   3 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.144625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.125027 restraints weight = 12509.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 2.38
r_work: 0.3531 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.1559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8558  Z= 0.130
  Angle     :  0.495   5.998  11594  Z= 0.266
  Chirality :  0.040   0.138   1317
  Planarity :  0.004   0.045   1466
  Dihedral  :  4.176  18.199   1139
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 16.92 %
    Favored  : 80.24 %
  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 are not related in a simple way.
  whole:  1.81 (0.26), residues: 1047
  helix:  2.96 (0.23), residues: 443
  sheet:  0.87 (0.34), residues: 217
  loop : -0.76 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 219 
 TYR   0.011   0.001   TYR B 289 
 PHE   0.013   0.001   PHE N 108 
 TRP   0.013   0.001   TRP R  97 
 HIS   0.003   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8558)
  covalent geometry    : angle       0.49538 (11594)
  hydrogen bonds       : bond        0.04120 (  484)
  hydrogen bonds       : angle       4.12242 ( 1407)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 276
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   22 PHE cc_start: 0.7621 (t80) cc_final: 0.7298 (t80)
REVERT: R  162 MET cc_start: 0.4569 (ptt) cc_final: 0.4164 (ptt)
REVERT: R  207 LYS cc_start: 0.8184 (ttpt) cc_final: 0.7928 (ttpt)
REVERT: R  285 LYS cc_start: 0.8503 (tmtt) cc_final: 0.8083 (tmtt)
REVERT: A   56 MET cc_start: 0.6780 (tpt) cc_final: 0.6556 (tpt)
REVERT: A  121 LEU cc_start: 0.7747 (tp) cc_final: 0.7447 (mt)
REVERT: A  123 GLU cc_start: 0.7692 (tt0) cc_final: 0.7300 (tt0)
REVERT: A  128 PHE cc_start: 0.8449 (t80) cc_final: 0.8217 (t80)
REVERT: A  188 ARG cc_start: 0.7954 (mtm-85) cc_final: 0.7614 (mtm-85)
REVERT: A  195 PHE cc_start: 0.8183 (t80) cc_final: 0.7772 (t80)
REVERT: A  202 ARG cc_start: 0.7786 (mtm180) cc_final: 0.7189 (mtm180)
REVERT: A  236 ASP cc_start: 0.8379 (t70) cc_final: 0.7962 (t0)
REVERT: B   25 CYS cc_start: 0.7842 (m) cc_final: 0.7445 (m)
REVERT: B   38 ASP cc_start: 0.7705 (m-30) cc_final: 0.7442 (m-30)
REVERT: B   49 ARG cc_start: 0.7639 (mpt90) cc_final: 0.7328 (mtt90)
REVERT: B   68 ARG cc_start: 0.8383 (ttt-90) cc_final: 0.8143 (ttt-90)
REVERT: B  190 LEU cc_start: 0.8689 (pp) cc_final: 0.8433 (pp)
REVERT: B  258 ASP cc_start: 0.8166 (t70) cc_final: 0.7783 (t70)
REVERT: G   25 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7689 (mp)
REVERT: G   38 MET cc_start: 0.6661 (ppp) cc_final: 0.6241 (ppp)
REVERT: N   80 TYR cc_start: 0.7769 (m-80) cc_final: 0.7491 (m-80)
REVERT: N  117 TYR cc_start: 0.8372 (m-80) cc_final: 0.7691 (m-80)
  outliers start: 26
  outliers final: 16
  residues processed: 284
  average time/residue: 0.1178
  time to fit residues: 42.7825
Evaluate side-chains
  286 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 269
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue  221 MET
Chi-restraints excluded: chain R residue  297 VAL
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue  111 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 100 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 84 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
R  21 ASN
R 176 ASN
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
N   3 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.143178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.123615 restraints weight = 12455.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 2.36
r_work: 0.3485 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8558  Z= 0.183
  Angle     :  0.534   6.313  11594  Z= 0.286
  Chirality :  0.042   0.146   1317
  Planarity :  0.004   0.045   1466
  Dihedral  :  4.343  20.260   1139
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 18.78 %
    Favored  : 78.60 %
  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 are not related in a simple way.
  whole:  1.67 (0.26), residues: 1047
  helix:  2.87 (0.23), residues: 441
  sheet:  0.75 (0.35), residues: 217
  loop : -0.82 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 219 
 TYR   0.012   0.001   TYR R 271 
 PHE   0.017   0.001   PHE B 235 
 TRP   0.018   0.001   TRP B 339 
 HIS   0.004   0.001   HIS R 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 8558)
  covalent geometry    : angle       0.53354 (11594)
  hydrogen bonds       : bond        0.04522 (  484)
  hydrogen bonds       : angle       4.22023 ( 1407)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 282
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   22 PHE cc_start: 0.7635 (t80) cc_final: 0.7300 (t80)
REVERT: R   24 ASN cc_start: 0.7874 (m-40) cc_final: 0.7580 (m-40)
REVERT: R  162 MET cc_start: 0.4557 (ptt) cc_final: 0.4144 (ptt)
REVERT: R  207 LYS cc_start: 0.8193 (ttpt) cc_final: 0.7931 (ttpt)
REVERT: R  285 LYS cc_start: 0.8527 (tmtt) cc_final: 0.8089 (tmtt)
REVERT: A   56 MET cc_start: 0.6844 (tpt) cc_final: 0.6584 (tpt)
REVERT: A  123 GLU cc_start: 0.7690 (tt0) cc_final: 0.7312 (tt0)
REVERT: A  128 PHE cc_start: 0.8459 (t80) cc_final: 0.8247 (t80)
REVERT: A  188 ARG cc_start: 0.8009 (mtm-85) cc_final: 0.7793 (mtm-85)
REVERT: A  195 PHE cc_start: 0.8286 (t80) cc_final: 0.7884 (t80)
REVERT: A  202 ARG cc_start: 0.7751 (mtm180) cc_final: 0.7149 (mtm180)
REVERT: A  236 ASP cc_start: 0.8336 (t70) cc_final: 0.7942 (t0)
REVERT: B   25 CYS cc_start: 0.7734 (m) cc_final: 0.7416 (m)
REVERT: B   49 ARG cc_start: 0.7706 (mpt90) cc_final: 0.7277 (mtt90)
REVERT: B   59 TYR cc_start: 0.7731 (OUTLIER) cc_final: 0.7492 (t80)
REVERT: B   68 ARG cc_start: 0.8360 (ttt-90) cc_final: 0.8064 (ttt-90)
REVERT: B  170 ASP cc_start: 0.7595 (t0) cc_final: 0.7336 (t0)
REVERT: B  190 LEU cc_start: 0.8702 (pp) cc_final: 0.8438 (pp)
REVERT: B  247 ASP cc_start: 0.7417 (m-30) cc_final: 0.7137 (m-30)
REVERT: G   25 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7711 (mp)
REVERT: G   38 MET cc_start: 0.6744 (ppp) cc_final: 0.6308 (ppp)
REVERT: N   80 TYR cc_start: 0.7782 (m-80) cc_final: 0.7510 (m-80)
REVERT: N  117 TYR cc_start: 0.8408 (m-80) cc_final: 0.8034 (m-80)
  outliers start: 24
  outliers final: 17
  residues processed: 289
  average time/residue: 0.1151
  time to fit residues: 42.7922
Evaluate side-chains
  297 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 278
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   21 ASN
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue  193 ILE
Chi-restraints excluded: chain R residue  297 VAL
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue  111 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 89 optimal weight:    0.0270
   chunk 45 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 69 optimal weight:    0.4980
   chunk 78 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.6240

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

Flipped N/Q/H residues before XYZ refinement:
R  21 ASN
A  78 GLN
B 239 ASN
N   3 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.143830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.124223 restraints weight = 12663.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 2.41
r_work: 0.3497 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8558  Z= 0.146
  Angle     :  0.522   8.012  11594  Z= 0.280
  Chirality :  0.041   0.149   1317
  Planarity :  0.004   0.044   1466
  Dihedral  :  4.279  20.215   1139
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 19.43 %
    Favored  : 78.17 %
  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 are not related in a simple way.
  whole:  1.69 (0.26), residues: 1047
  helix:  2.91 (0.23), residues: 442
  sheet:  0.76 (0.35), residues: 217
  loop : -0.85 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 219 
 TYR   0.010   0.001   TYR B 289 
 PHE   0.013   0.001   PHE N 108 
 TRP   0.014   0.001   TRP A  99 
 HIS   0.003   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 8558)
  covalent geometry    : angle       0.52218 (11594)
  hydrogen bonds       : bond        0.04271 (  484)
  hydrogen bonds       : angle       4.14642 ( 1407)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 279
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   22 PHE cc_start: 0.7652 (t80) cc_final: 0.7307 (t80)
REVERT: R   24 ASN cc_start: 0.7837 (m-40) cc_final: 0.7546 (m-40)
REVERT: R  207 LYS cc_start: 0.8181 (ttpt) cc_final: 0.7909 (ttpt)
REVERT: R  285 LYS cc_start: 0.8494 (tmtt) cc_final: 0.8064 (tmtt)
REVERT: A   56 MET cc_start: 0.6813 (tpt) cc_final: 0.6556 (tpt)
REVERT: A  121 LEU cc_start: 0.7776 (tp) cc_final: 0.7476 (mt)
REVERT: A  123 GLU cc_start: 0.7664 (tt0) cc_final: 0.7285 (tt0)
REVERT: A  128 PHE cc_start: 0.8452 (t80) cc_final: 0.8240 (t80)
REVERT: A  188 ARG cc_start: 0.8003 (mtm-85) cc_final: 0.7751 (mtm-85)
REVERT: A  195 PHE cc_start: 0.8249 (t80) cc_final: 0.7826 (t80)
REVERT: A  202 ARG cc_start: 0.7706 (mtm180) cc_final: 0.7121 (mtm180)
REVERT: A  236 ASP cc_start: 0.8345 (t70) cc_final: 0.7942 (t0)
REVERT: B   25 CYS cc_start: 0.7707 (m) cc_final: 0.7389 (m)
REVERT: B   49 ARG cc_start: 0.7733 (mpt90) cc_final: 0.7335 (mtt90)
REVERT: B   59 TYR cc_start: 0.7735 (OUTLIER) cc_final: 0.7520 (t80)
REVERT: B   68 ARG cc_start: 0.8348 (ttt-90) cc_final: 0.8037 (ttt-90)
REVERT: B  190 LEU cc_start: 0.8701 (pp) cc_final: 0.8426 (pp)
REVERT: B  247 ASP cc_start: 0.7398 (m-30) cc_final: 0.7117 (m-30)
REVERT: G   25 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7702 (mp)
REVERT: G   38 MET cc_start: 0.6780 (ppp) cc_final: 0.6339 (ppp)
REVERT: N   80 TYR cc_start: 0.7749 (m-80) cc_final: 0.7497 (m-80)
REVERT: N  117 TYR cc_start: 0.8367 (m-80) cc_final: 0.8093 (m-80)
  outliers start: 22
  outliers final: 19
  residues processed: 285
  average time/residue: 0.1165
  time to fit residues: 42.3953
Evaluate side-chains
  294 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 273
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   21 ASN
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue  123 ARG
Chi-restraints excluded: chain R residue  221 MET
Chi-restraints excluded: chain R residue  297 VAL
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue  111 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 21 optimal weight:    0.4980
   chunk 32 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
R  21 ASN
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
N   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.142829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.123224 restraints weight = 12422.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 2.39
r_work: 0.3482 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8558  Z= 0.178
  Angle     :  0.546   8.724  11594  Z= 0.292
  Chirality :  0.042   0.154   1317
  Planarity :  0.004   0.045   1466
  Dihedral  :  4.338  20.015   1139
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.21 %
    Favored  : 77.62 %
  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 are not related in a simple way.
  whole:  1.60 (0.26), residues: 1047
  helix:  2.79 (0.23), residues: 442
  sheet:  0.70 (0.35), residues: 219
  loop : -0.83 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 219 
 TYR   0.011   0.001   TYR R 271 
 PHE   0.015   0.001   PHE B 235 
 TRP   0.015   0.001   TRP A  99 
 HIS   0.004   0.001   HIS R 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 8558)
  covalent geometry    : angle       0.54581 (11594)
  hydrogen bonds       : bond        0.04456 (  484)
  hydrogen bonds       : angle       4.19798 ( 1407)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 284
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   22 PHE cc_start: 0.7700 (t80) cc_final: 0.7393 (t80)
REVERT: R   24 ASN cc_start: 0.7855 (m-40) cc_final: 0.7561 (m-40)
REVERT: R  122 LYS cc_start: 0.8120 (tppt) cc_final: 0.7785 (tptp)
REVERT: R  184 ASN cc_start: 0.8474 (m-40) cc_final: 0.8267 (m-40)
REVERT: R  207 LYS cc_start: 0.8187 (ttpt) cc_final: 0.7922 (ttpt)
REVERT: R  285 LYS cc_start: 0.8508 (tmtt) cc_final: 0.8073 (tmtt)
REVERT: A   56 MET cc_start: 0.6835 (tpt) cc_final: 0.6574 (tpt)
REVERT: A   76 LYS cc_start: 0.7964 (mtpp) cc_final: 0.7691 (mtpp)
REVERT: A  121 LEU cc_start: 0.7800 (tp) cc_final: 0.7500 (mt)
REVERT: A  123 GLU cc_start: 0.7675 (tt0) cc_final: 0.7299 (tt0)
REVERT: A  128 PHE cc_start: 0.8460 (t80) cc_final: 0.8239 (t80)
REVERT: A  188 ARG cc_start: 0.8013 (mtm-85) cc_final: 0.7731 (mtm-85)
REVERT: A  195 PHE cc_start: 0.8297 (t80) cc_final: 0.7891 (t80)
REVERT: A  202 ARG cc_start: 0.7719 (mtm180) cc_final: 0.7153 (mtm180)
REVERT: A  236 ASP cc_start: 0.8339 (t70) cc_final: 0.7945 (t0)
REVERT: B   25 CYS cc_start: 0.7715 (m) cc_final: 0.7387 (m)
REVERT: B   49 ARG cc_start: 0.7762 (mpt90) cc_final: 0.7374 (mtt90)
REVERT: B   68 ARG cc_start: 0.8353 (ttt-90) cc_final: 0.8108 (ttt-90)
REVERT: B  190 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8424 (pp)
REVERT: B  234 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8244 (m-80)
REVERT: B  247 ASP cc_start: 0.7413 (m-30) cc_final: 0.7138 (m-30)
REVERT: G   38 MET cc_start: 0.6754 (ppp) cc_final: 0.6323 (ppp)
REVERT: N   80 TYR cc_start: 0.7764 (m-80) cc_final: 0.7439 (m-80)
REVERT: N  117 TYR cc_start: 0.8394 (m-80) cc_final: 0.8182 (m-80)
  outliers start: 29
  outliers final: 21
  residues processed: 292
  average time/residue: 0.1187
  time to fit residues: 44.2846
Evaluate side-chains
  304 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 281
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   21 ASN
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue  123 ARG
Chi-restraints excluded: chain R residue  143 HIS
Chi-restraints excluded: chain R residue  177 THR
Chi-restraints excluded: chain R residue  193 ILE
Chi-restraints excluded: chain R residue  297 VAL
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue  111 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0970
   chunk 51 optimal weight:    0.6980
   chunk 58 optimal weight:    0.4980
   chunk 14 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
R  21 ASN
R 184 ASN
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 119 ASN
B 239 ASN
N   3 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.143389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.123907 restraints weight = 12574.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 2.40
r_work: 0.3516 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8558  Z= 0.149
  Angle     :  0.529   7.022  11594  Z= 0.285
  Chirality :  0.041   0.160   1317
  Planarity :  0.004   0.044   1466
  Dihedral  :  4.292  19.829   1139
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 20.31 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.61 (0.26), residues: 1047
  helix:  2.81 (0.23), residues: 444
  sheet:  0.70 (0.35), residues: 217
  loop : -0.86 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 219 
 TYR   0.012   0.001   TYR B 289 
 PHE   0.013   0.001   PHE N 108 
 TRP   0.019   0.001   TRP B 339 
 HIS   0.003   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 8558)
  covalent geometry    : angle       0.52901 (11594)
  hydrogen bonds       : bond        0.04294 (  484)
  hydrogen bonds       : angle       4.14898 ( 1407)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 277
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   22 PHE cc_start: 0.7663 (t80) cc_final: 0.7332 (t80)
REVERT: R   24 ASN cc_start: 0.7861 (m-40) cc_final: 0.7572 (m-40)
REVERT: R  122 LYS cc_start: 0.8127 (tppt) cc_final: 0.7804 (tptp)
REVERT: R  207 LYS cc_start: 0.8189 (ttpt) cc_final: 0.7925 (ttpt)
REVERT: R  285 LYS cc_start: 0.8486 (tmtt) cc_final: 0.8077 (tmtt)
REVERT: A   56 MET cc_start: 0.6807 (tpt) cc_final: 0.6553 (tpt)
REVERT: A   76 LYS cc_start: 0.7965 (mtpp) cc_final: 0.7693 (mtpp)
REVERT: A  121 LEU cc_start: 0.7783 (tp) cc_final: 0.7488 (mt)
REVERT: A  123 GLU cc_start: 0.7643 (tt0) cc_final: 0.7266 (tt0)
REVERT: A  128 PHE cc_start: 0.8464 (t80) cc_final: 0.8245 (t80)
REVERT: A  188 ARG cc_start: 0.7995 (mtm-85) cc_final: 0.7702 (mtm-85)
REVERT: A  195 PHE cc_start: 0.8272 (t80) cc_final: 0.7882 (t80)
REVERT: A  202 ARG cc_start: 0.7697 (mtm180) cc_final: 0.7130 (mtm180)
REVERT: A  236 ASP cc_start: 0.8333 (t70) cc_final: 0.7942 (t0)
REVERT: B   25 CYS cc_start: 0.7693 (m) cc_final: 0.7382 (m)
REVERT: B   49 ARG cc_start: 0.7752 (mpt90) cc_final: 0.7340 (mtt90)
REVERT: B   68 ARG cc_start: 0.8347 (ttt-90) cc_final: 0.8042 (ttt-90)
REVERT: B  190 LEU cc_start: 0.8693 (pp) cc_final: 0.8413 (pp)
REVERT: B  234 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8195 (m-80)
REVERT: B  247 ASP cc_start: 0.7407 (m-30) cc_final: 0.7129 (m-30)
REVERT: G   38 MET cc_start: 0.6765 (ppp) cc_final: 0.6331 (ppp)
REVERT: N   80 TYR cc_start: 0.7756 (m-80) cc_final: 0.7438 (m-80)
  outliers start: 23
  outliers final: 20
  residues processed: 282
  average time/residue: 0.1069
  time to fit residues: 38.5430
Evaluate side-chains
  295 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 274
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   21 ASN
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue  143 HIS
Chi-restraints excluded: chain R residue  193 ILE
Chi-restraints excluded: chain R residue  221 MET
Chi-restraints excluded: chain R residue  297 VAL
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  119 ASN
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue  111 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
R  21 ASN
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
N   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.143233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.123608 restraints weight = 12504.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 2.40
r_work: 0.3508 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8558  Z= 0.166
  Angle     :  0.539   7.296  11594  Z= 0.290
  Chirality :  0.042   0.164   1317
  Planarity :  0.004   0.044   1466
  Dihedral  :  4.309  19.839   1139
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 20.20 %
    Favored  : 77.29 %
  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 are not related in a simple way.
  whole:  1.57 (0.26), residues: 1047
  helix:  2.76 (0.23), residues: 444
  sheet:  0.68 (0.35), residues: 217
  loop : -0.85 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 256 
 TYR   0.011   0.001   TYR B 289 
 PHE   0.012   0.001   PHE N 108 
 TRP   0.018   0.001   TRP B 339 
 HIS   0.004   0.001   HIS R 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 8558)
  covalent geometry    : angle       0.53942 (11594)
  hydrogen bonds       : bond        0.04351 (  484)
  hydrogen bonds       : angle       4.16203 ( 1407)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 277
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   22 PHE cc_start: 0.7604 (t80) cc_final: 0.7268 (t80)
REVERT: R   24 ASN cc_start: 0.7850 (m-40) cc_final: 0.7551 (m-40)
REVERT: R  207 LYS cc_start: 0.8197 (ttpt) cc_final: 0.7935 (ttpt)
REVERT: R  285 LYS cc_start: 0.8498 (tmtt) cc_final: 0.8092 (tmtt)
REVERT: A   56 MET cc_start: 0.6815 (tpt) cc_final: 0.6560 (tpt)
REVERT: A   76 LYS cc_start: 0.7969 (mtpp) cc_final: 0.7695 (mtpp)
REVERT: A  121 LEU cc_start: 0.7797 (tp) cc_final: 0.7493 (mt)
REVERT: A  123 GLU cc_start: 0.7731 (tt0) cc_final: 0.7350 (tt0)
REVERT: A  128 PHE cc_start: 0.8466 (t80) cc_final: 0.8245 (t80)
REVERT: A  188 ARG cc_start: 0.8006 (mtm-85) cc_final: 0.7711 (mtm-85)
REVERT: A  195 PHE cc_start: 0.8279 (t80) cc_final: 0.7881 (t80)
REVERT: A  202 ARG cc_start: 0.7704 (mtm180) cc_final: 0.7151 (mtm180)
REVERT: A  236 ASP cc_start: 0.8341 (t70) cc_final: 0.7927 (t0)
REVERT: B   25 CYS cc_start: 0.7720 (m) cc_final: 0.7406 (m)
REVERT: B   49 ARG cc_start: 0.7757 (mpt90) cc_final: 0.7371 (mtt90)
REVERT: B   68 ARG cc_start: 0.8336 (ttt-90) cc_final: 0.8051 (ttt-90)
REVERT: B  190 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8410 (pp)
REVERT: B  234 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8151 (m-80)
REVERT: B  247 ASP cc_start: 0.7428 (m-30) cc_final: 0.7146 (m-30)
REVERT: B  283 ARG cc_start: 0.8308 (tpt-90) cc_final: 0.8025 (tpt-90)
REVERT: G   38 MET cc_start: 0.6756 (ppp) cc_final: 0.6317 (ppp)
REVERT: N   80 TYR cc_start: 0.7765 (m-80) cc_final: 0.7440 (m-80)
  outliers start: 23
  outliers final: 20
  residues processed: 282
  average time/residue: 0.1164
  time to fit residues: 41.8139
Evaluate side-chains
  299 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 277
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   21 ASN
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue  143 HIS
Chi-restraints excluded: chain R residue  193 ILE
Chi-restraints excluded: chain R residue  221 MET
Chi-restraints excluded: chain R residue  297 VAL
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  119 ASN
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue  111 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9990
   chunk 82 optimal weight:    0.2980
   chunk 0 optimal weight:    7.9990
   chunk 96 optimal weight:    0.4980
   chunk 97 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0870
   chunk 27 optimal weight:    0.6980
   chunk 80 optimal weight:    0.2980
   overall best weight:    0.3758

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

Flipped N/Q/H residues before XYZ refinement:
R  21 ASN
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 119 ASN
B 239 ASN
N   3 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.144505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.125000 restraints weight = 12534.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.3673 rms_B_bonded: 2.41
r_work: 0.3546 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.1946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8558  Z= 0.121
  Angle     :  0.521   8.368  11594  Z= 0.279
  Chirality :  0.041   0.176   1317
  Planarity :  0.003   0.045   1466
  Dihedral  :  4.204  19.521   1139
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 20.85 %
    Favored  : 76.97 %
  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 are not related in a simple way.
  whole:  1.63 (0.26), residues: 1047
  helix:  2.89 (0.23), residues: 444
  sheet:  0.74 (0.35), residues: 212
  loop : -0.92 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 219 
 TYR   0.012   0.001   TYR B 289 
 PHE   0.013   0.001   PHE A  77 
 TRP   0.017   0.001   TRP R  97 
 HIS   0.004   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8558)
  covalent geometry    : angle       0.52120 (11594)
  hydrogen bonds       : bond        0.04030 (  484)
  hydrogen bonds       : angle       4.08497 ( 1407)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2008.21 seconds
wall clock time: 35 minutes 6.29 seconds (2106.29 seconds total)