Starting phenix.real_space_refine
on Wed Sep 17 07:50:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j0f_61054/09_2025/9j0f_61054.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j0f_61054/09_2025/9j0f_61054.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j0f_61054/09_2025/9j0f_61054.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j0f_61054/09_2025/9j0f_61054.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j0f_61054/09_2025/9j0f_61054.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j0f_61054/09_2025/9j0f_61054.map"
  }
  resolution = 2.76
  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=   0.069
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      47      5.16       5
     C    4434      2.51       5
     N    1153      2.21       5
     O    1219      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6855
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1615
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 135
          Unresolved non-hydrogen angles: 165
          Unresolved non-hydrogen dihedrals: 105
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 12, 'ARG:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 89
    Chain: "B"
      Number of atoms: 2475
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2475
          Classifications: {'peptide': 337}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 116
          Unresolved non-hydrogen angles: 141
          Unresolved non-hydrogen dihedrals: 91
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 3, 'ARG:plan': 7, 'GLU:plan': 5, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 91
    Chain: "G"
      Number of atoms: 377
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 377
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 52
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 4, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 28
    Chain: "R"
      Number of atoms: 2344
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2344
          Classifications: {'peptide': 295}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 10, 'TRANS': 284}
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 95
          Unresolved non-hydrogen dihedrals: 63
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 3, 'ARG:plan': 3, 'GLU:plan': 4}
          Unresolved non-hydrogen planarities: 46
    Chain: "R"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'NAI': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.95, per 1000 atoms: 0.28
  Number of scatterers: 6855
  At special positions: 0
  Unit cell: (70.72, 98.176, 128.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      47     16.00
     P       2     15.00
     O    1219      8.00
     N    1153      7.00
     C    4434      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  94 " - pdb=" SG  CYS R 172 " distance=2.03

  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: 0.64
  Conformation dependent library (CDL) restraints added in 490.5 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1720

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 8 sheets defined
      46.6% alpha, 18.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.747A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 52
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.555A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.664A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 3.676A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.784A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.548A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 5 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 8 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'R' and resid 24 through 48
      removed outlier: 4.324A  pdb=" N   LEU R  39 " --> pdb=" O   ALA R  35 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 54 through 83
      Proline residue:  R  75  - end of helix
    Processing helix  chain 'R' and resid 87 through 96
    Processing helix  chain 'R' and resid 96 through 125
    Processing helix  chain 'R' and resid 137 through 154
      removed outlier: 3.568A  pdb=" N   LEU R 141 " --> pdb=" O   TYR R 137 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 154 through 159
    Processing helix  chain 'R' and resid 177 through 215
    Processing helix  chain 'R' and resid 221 through 251
      Proline residue:  R 248  - end of helix
    Processing helix  chain 'R' and resid 252 through 261
    Processing helix  chain 'R' and resid 268 through 286
      removed outlier: 3.726A  pdb=" N   ARG R 274 " --> pdb=" O   LYS R 270 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 286 through 291
    Processing helix  chain 'R' and resid 299 through 310
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.742A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.595A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.697A  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: 6.417A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 152
      removed outlier: 3.724A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.866A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.899A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.213A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.481A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.637A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 5.939A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    407 hydrogen bonds defined for protein.
    1170 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: 1.19

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1606
        1.33 -     1.45: 1483
        1.45 -     1.57: 3850
        1.57 -     1.69: 4
        1.69 -     1.81: 66
  Bond restraints: 7009
  Sorted by residual:
  bond pdb=" C4A NAI R 401 "
       pdb=" C5A NAI R 401 "
    ideal  model  delta    sigma   weight residual
    1.386  1.472 -0.086 2.00e-02 2.50e+03 1.85e+01
  bond pdb=" CA  LYS R  77 "
       pdb=" C   LYS R  77 "
    ideal  model  delta    sigma   weight residual
    1.524  1.473  0.051 1.24e-02 6.50e+03 1.71e+01
  bond pdb=" CA  ASN R 188 "
       pdb=" CB  ASN R 188 "
    ideal  model  delta    sigma   weight residual
    1.530  1.470  0.060 1.57e-02 4.06e+03 1.44e+01
  bond pdb=" C5A NAI R 401 "
       pdb=" C6A NAI R 401 "
    ideal  model  delta    sigma   weight residual
    1.404  1.480 -0.076 2.00e-02 2.50e+03 1.44e+01
  bond pdb=" C6N NAI R 401 "
       pdb=" N1N NAI R 401 "
    ideal  model  delta    sigma   weight residual
    1.394  1.334  0.060 2.00e-02 2.50e+03 8.86e+00
  ... (remaining 7004 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 9379
        1.85 -     3.71: 133
        3.71 -     5.56: 20
        5.56 -     7.42: 5
        7.42 -     9.27: 3
  Bond angle restraints: 9540
  Sorted by residual:
  angle pdb=" C2A NAI R 401 "
        pdb=" N3A NAI R 401 "
        pdb=" C4A NAI R 401 "
      ideal   model   delta    sigma   weight residual
     111.83  121.10   -9.27 3.00e+00 1.11e-01 9.55e+00
  angle pdb=" N   LYS R  77 "
        pdb=" CA  LYS R  77 "
        pdb=" C   LYS R  77 "
      ideal   model   delta    sigma   weight residual
     110.97  107.68    3.29 1.09e+00 8.42e-01 9.10e+00
  angle pdb=" N   ARG R 274 "
        pdb=" CA  ARG R 274 "
        pdb=" C   ARG R 274 "
      ideal   model   delta    sigma   weight residual
     112.23  108.68    3.55 1.26e+00 6.30e-01 7.93e+00
  angle pdb=" C5A NAI R 401 "
        pdb=" C4A NAI R 401 "
        pdb=" N3A NAI R 401 "
      ideal   model   delta    sigma   weight residual
     126.33  118.21    8.12 3.00e+00 1.11e-01 7.33e+00
  angle pdb=" PA  NAI R 401 "
        pdb=" O3  NAI R 401 "
        pdb=" PN  NAI R 401 "
      ideal   model   delta    sigma   weight residual
     129.27  121.23    8.04 3.00e+00 1.11e-01 7.19e+00
  ... (remaining 9535 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 3755
       17.47 -    34.93: 323
       34.93 -    52.40: 39
       52.40 -    69.86: 12
       69.86 -    87.33: 7
  Dihedral angle restraints: 4136
    sinusoidal: 1487
      harmonic: 2649
  Sorted by residual:
  dihedral pdb=" CA  GLY R  85 "
           pdb=" C   GLY R  85 "
           pdb=" N   PRO R  86 "
           pdb=" CA  PRO R  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.55   32.45     0      5.00e+00 4.00e-02 4.21e+01
  dihedral pdb=" CA  GLU R 262 "
           pdb=" C   GLU R 262 "
           pdb=" N   ALA R 263 "
           pdb=" CA  ALA R 263 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.69   23.31     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" CA  THR B 249 "
           pdb=" C   THR B 249 "
           pdb=" N   CYS B 250 "
           pdb=" CA  CYS B 250 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.06   18.94     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 4133 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 905
       0.051 -    0.102: 192
       0.102 -    0.153: 28
       0.153 -    0.205: 1
       0.205 -    0.256: 1
  Chirality restraints: 1127
  Sorted by residual:
  chirality pdb=" C1B NAI R 401 "
            pdb=" C2B NAI R 401 "
            pdb=" N9A NAI R 401 "
            pdb=" O4B NAI R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.31    2.57   -0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" CB  ILE R  20 "
            pdb=" CA  ILE R  20 "
            pdb=" CG1 ILE R  20 "
            pdb=" CG2 ILE R  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.80e-01
  chirality pdb=" CA  ILE B 123 "
            pdb=" N   ILE B 123 "
            pdb=" C   ILE B 123 "
            pdb=" CB  ILE B 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.84e-01
  ... (remaining 1124 not shown)

  Planarity restraints: 1178
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG R 274 "    0.303 9.50e-02 1.11e+02   1.36e-01 1.13e+01
        pdb=" NE  ARG R 274 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG R 274 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG R 274 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG R 274 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 273 "    0.008 2.00e-02 2.50e+03   1.57e-02 2.45e+00
        pdb=" C   LEU R 273 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   LEU R 273 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ARG R 274 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.021 5.00e-02 4.00e+02   3.11e-02 1.54e+00
        pdb=" N   PRO B 236 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1175 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 78
        2.64 -     3.20: 6335
        3.20 -     3.77: 11366
        3.77 -     4.33: 15957
        4.33 -     4.90: 26036
  Nonbonded interactions: 59772
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.069 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OD1 ASP R 118 "
            pdb=" OG  SER R 134 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD2 ASP B 163 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" N   ASN R  17 "
            pdb=" OH  TYR R 275 "
     model   vdw
     2.261 3.120
  ... (remaining 59767 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:             2.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.140
  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:6.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
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   0.086   7010  Z= 0.219
  Angle     :  0.591   9.272   9542  Z= 0.304
  Chirality :  0.042   0.256   1127
  Planarity :  0.005   0.136   1178
  Dihedral  : 13.670  87.327   2413
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.29 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.28), residues: 893
  helix:  1.84 (0.26), residues: 394
  sheet:  0.26 (0.38), residues: 167
  loop : -0.63 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 304 
 TYR   0.015   0.001   TYR R 106 
 PHE   0.018   0.001   PHE R 195 
 TRP   0.014   0.002   TRP B  82 
 HIS   0.006   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 7009)
  covalent geometry    : angle       0.59007 ( 9540)
  SS BOND              : bond        0.00312 (    1)
  SS BOND              : angle       1.78915 (    2)
  hydrogen bonds       : bond        0.11998 (  407)
  hydrogen bonds       : angle       5.45645 ( 1170)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 143
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: B   96 ARG cc_start: 0.7725 (mtt180) cc_final: 0.7419 (mtt90)
  outliers start: 1
  outliers final: 0
  residues processed: 143
  average time/residue: 0.4674
  time to fit residues: 71.2211
Evaluate side-chains
  102 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0570
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0470
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
A 322 HIS
B 142 HIS
B 156 GLN
B 293 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  18 GLN
R  90 ASN
R 217 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.217966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.163320 restraints weight = 7535.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3920 rms_B_bonded: 1.90
r_work: 0.3838 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3727 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7010  Z= 0.134
  Angle     :  0.534   7.559   9542  Z= 0.285
  Chirality :  0.042   0.147   1127
  Planarity :  0.003   0.038   1178
  Dihedral  :  7.393  84.161   1020
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 11.47 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.29), residues: 893
  helix:  1.87 (0.26), residues: 398
  sheet:  0.33 (0.38), residues: 172
  loop : -0.56 (0.36), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 150 
 TYR   0.016   0.001   TYR R 256 
 PHE   0.020   0.001   PHE R 195 
 TRP   0.018   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7009)
  covalent geometry    : angle       0.53344 ( 9540)
  SS BOND              : bond        0.00081 (    1)
  SS BOND              : angle       0.86450 (    2)
  hydrogen bonds       : bond        0.04225 (  407)
  hydrogen bonds       : angle       4.64269 ( 1170)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.7636 (m-30) cc_final: 0.7424 (m-30)
REVERT: A  240 MET cc_start: 0.5958 (OUTLIER) cc_final: 0.4880 (ttm)
REVERT: A  340 THR cc_start: 0.8227 (m) cc_final: 0.8005 (m)
REVERT: A  343 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7752 (mp)
REVERT: B   96 ARG cc_start: 0.8194 (mtt180) cc_final: 0.7892 (mtt90)
REVERT: B  263 THR cc_start: 0.8576 (t) cc_final: 0.8118 (m)
REVERT: R  121 TYR cc_start: 0.7462 (t80) cc_final: 0.6830 (t80)
REVERT: R  229 LYS cc_start: 0.7264 (tppt) cc_final: 0.6954 (mptt)
  outliers start: 15
  outliers final: 6
  residues processed: 107
  average time/residue: 0.4368
  time to fit residues: 50.0395
Evaluate side-chains
  100 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 38 optimal weight:    0.0670
   chunk 55 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    1.2124

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
B 156 GLN
B 293 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.212401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.156194 restraints weight = 7411.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3857 rms_B_bonded: 1.89
r_work: 0.3776 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3666 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   7010  Z= 0.216
  Angle     :  0.594   7.597   9542  Z= 0.312
  Chirality :  0.043   0.151   1127
  Planarity :  0.004   0.036   1178
  Dihedral  :  7.146  68.856   1020
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 13.93 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.29), residues: 893
  helix:  1.69 (0.26), residues: 404
  sheet:  0.24 (0.38), residues: 178
  loop : -0.59 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 251 
 TYR   0.014   0.002   TYR R 106 
 PHE   0.019   0.002   PHE R 195 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 ( 7009)
  covalent geometry    : angle       0.59390 ( 9540)
  SS BOND              : bond        0.00015 (    1)
  SS BOND              : angle       0.72372 (    2)
  hydrogen bonds       : bond        0.04419 (  407)
  hydrogen bonds       : angle       4.76087 ( 1170)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A  240 MET cc_start: 0.6203 (OUTLIER) cc_final: 0.5168 (ttm)
REVERT: A  337 ASP cc_start: 0.8161 (m-30) cc_final: 0.7926 (m-30)
REVERT: B   96 ARG cc_start: 0.8259 (mtt180) cc_final: 0.7985 (mtt90)
REVERT: R  121 TYR cc_start: 0.7574 (t80) cc_final: 0.6950 (t80)
REVERT: R  229 LYS cc_start: 0.7382 (tppt) cc_final: 0.6791 (mmtt)
  outliers start: 20
  outliers final: 9
  residues processed: 110
  average time/residue: 0.4482
  time to fit residues: 52.7011
Evaluate side-chains
  106 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   96 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 79 optimal weight:    8.9990
   chunk 52 optimal weight:    0.0870
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.223477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.180201 restraints weight = 7439.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.4146 rms_B_bonded: 1.79
r_work: 0.3939 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3826 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7010  Z= 0.150
  Angle     :  0.544   7.535   9542  Z= 0.287
  Chirality :  0.041   0.140   1127
  Planarity :  0.003   0.034   1178
  Dihedral  :  6.944  63.597   1020
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.55 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.29), residues: 893
  helix:  1.79 (0.26), residues: 404
  sheet:  0.15 (0.37), residues: 178
  loop : -0.57 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 134 
 TYR   0.017   0.001   TYR R 256 
 PHE   0.020   0.001   PHE R 195 
 TRP   0.019   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 7009)
  covalent geometry    : angle       0.54375 ( 9540)
  SS BOND              : bond        0.00019 (    1)
  SS BOND              : angle       0.84906 (    2)
  hydrogen bonds       : bond        0.04018 (  407)
  hydrogen bonds       : angle       4.58515 ( 1170)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A  216 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7872 (tt0)
REVERT: A  240 MET cc_start: 0.6233 (OUTLIER) cc_final: 0.5150 (ttm)
REVERT: A  318 GLU cc_start: 0.8383 (tt0) cc_final: 0.8168 (tt0)
REVERT: A  343 ILE cc_start: 0.8438 (mt) cc_final: 0.8069 (mp)
REVERT: B   96 ARG cc_start: 0.8348 (mtt180) cc_final: 0.7996 (mtt180)
REVERT: B  263 THR cc_start: 0.8657 (t) cc_final: 0.8220 (m)
REVERT: R  121 TYR cc_start: 0.7601 (t80) cc_final: 0.7010 (t80)
REVERT: R  122 LYS cc_start: 0.7783 (mtpp) cc_final: 0.7197 (mtmm)
REVERT: R  229 LYS cc_start: 0.7396 (tppt) cc_final: 0.7079 (mptt)
REVERT: R  232 SER cc_start: 0.7082 (m) cc_final: 0.6625 (t)
  outliers start: 17
  outliers final: 11
  residues processed: 110
  average time/residue: 0.4702
  time to fit residues: 55.1082
Evaluate side-chains
  110 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   96 VAL
Chi-restraints excluded: chain R residue  272 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0270
   chunk 33 optimal weight:    0.6980
   chunk 83 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 15 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 21 optimal weight:    8.9990
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.223766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.180524 restraints weight = 7537.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.4150 rms_B_bonded: 1.87
r_work: 0.3944 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3828 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.2467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7010  Z= 0.144
  Angle     :  0.535   8.063   9542  Z= 0.281
  Chirality :  0.041   0.139   1127
  Planarity :  0.003   0.035   1178
  Dihedral  :  6.796  59.540   1020
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 17.56 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.29), residues: 893
  helix:  1.86 (0.26), residues: 405
  sheet:  0.28 (0.38), residues: 172
  loop : -0.61 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 134 
 TYR   0.010   0.001   TYR A 320 
 PHE   0.020   0.001   PHE R 195 
 TRP   0.018   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 7009)
  covalent geometry    : angle       0.53440 ( 9540)
  SS BOND              : bond        0.00075 (    1)
  SS BOND              : angle       0.93744 (    2)
  hydrogen bonds       : bond        0.03888 (  407)
  hydrogen bonds       : angle       4.52849 ( 1170)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  216 GLU cc_start: 0.8097 (tt0) cc_final: 0.7863 (tt0)
REVERT: A  240 MET cc_start: 0.6215 (OUTLIER) cc_final: 0.5133 (ttm)
REVERT: A  343 ILE cc_start: 0.8425 (mt) cc_final: 0.8076 (mp)
REVERT: B   96 ARG cc_start: 0.8304 (mtt180) cc_final: 0.8056 (mtt90)
REVERT: B  263 THR cc_start: 0.8606 (t) cc_final: 0.8152 (m)
REVERT: R  121 TYR cc_start: 0.7609 (t80) cc_final: 0.7035 (t80)
REVERT: R  122 LYS cc_start: 0.7829 (mtpp) cc_final: 0.7208 (mtmm)
REVERT: R  229 LYS cc_start: 0.7365 (tppt) cc_final: 0.7064 (mptt)
  outliers start: 16
  outliers final: 9
  residues processed: 107
  average time/residue: 0.4351
  time to fit residues: 49.8267
Evaluate side-chains
  107 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue   24 ILE
Chi-restraints excluded: chain R residue   96 VAL
Chi-restraints excluded: chain R residue  272 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 37 optimal weight:    0.1980
   chunk 33 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0980
   chunk 26 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0770
   chunk 29 optimal weight:    0.2980
   chunk 76 optimal weight:    0.3980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.2138

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4630 r_free = 0.4630 target = 0.227109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.185095 restraints weight = 7532.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.4195 rms_B_bonded: 1.83
r_work: 0.3992 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3879 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.2657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7010  Z= 0.104
  Angle     :  0.494   7.731   9542  Z= 0.265
  Chirality :  0.041   0.219   1127
  Planarity :  0.003   0.036   1178
  Dihedral  :  6.499  54.281   1020
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 17.71 %
    Favored  : 79.97 %
  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 aren not related in a simple way.
  whole:  1.20 (0.29), residues: 893
  helix:  2.02 (0.26), residues: 407
  sheet:  0.26 (0.37), residues: 172
  loop : -0.48 (0.37), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 134 
 TYR   0.016   0.001   TYR R 256 
 PHE   0.024   0.001   PHE R 236 
 TRP   0.020   0.001   TRP B  82 
 HIS   0.002   0.000   HIS R 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 7009)
  covalent geometry    : angle       0.49333 ( 9540)
  SS BOND              : bond        0.00192 (    1)
  SS BOND              : angle       1.05435 (    2)
  hydrogen bonds       : bond        0.03523 (  407)
  hydrogen bonds       : angle       4.32230 ( 1170)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A  216 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7841 (tt0)
REVERT: A  240 MET cc_start: 0.6147 (OUTLIER) cc_final: 0.4988 (ttm)
REVERT: A  343 ILE cc_start: 0.8323 (mt) cc_final: 0.8110 (mp)
REVERT: B   96 ARG cc_start: 0.8254 (mtt180) cc_final: 0.7940 (mtt180)
REVERT: R   78 ILE cc_start: 0.7008 (pp) cc_final: 0.6754 (tt)
REVERT: R  121 TYR cc_start: 0.7541 (t80) cc_final: 0.6996 (t80)
REVERT: R  229 LYS cc_start: 0.7367 (tppt) cc_final: 0.7067 (mptt)
  outliers start: 16
  outliers final: 7
  residues processed: 116
  average time/residue: 0.4636
  time to fit residues: 57.3725
Evaluate side-chains
  105 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain R residue   96 VAL
Chi-restraints excluded: chain R residue  172 CYS
Chi-restraints excluded: chain R residue  272 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9990
   chunk 73 optimal weight:    0.3980
   chunk 17 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 80 optimal weight:    5.9990
   chunk 52 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 39 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
B 156 GLN
B 293 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4605 r_free = 0.4605 target = 0.224476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.181451 restraints weight = 7407.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.4162 rms_B_bonded: 1.82
r_work: 0.3965 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3852 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.2684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7010  Z= 0.144
  Angle     :  0.540   7.699   9542  Z= 0.284
  Chirality :  0.042   0.149   1127
  Planarity :  0.003   0.033   1178
  Dihedral  :  6.555  54.092   1020
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 18.58 %
    Favored  : 78.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.29), residues: 893
  helix:  1.92 (0.26), residues: 404
  sheet:  0.26 (0.37), residues: 177
  loop : -0.63 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 134 
 TYR   0.011   0.001   TYR R  49 
 PHE   0.019   0.001   PHE R 195 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 7009)
  covalent geometry    : angle       0.54039 ( 9540)
  SS BOND              : bond        0.00097 (    1)
  SS BOND              : angle       0.87742 (    2)
  hydrogen bonds       : bond        0.03744 (  407)
  hydrogen bonds       : angle       4.45959 ( 1170)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A  240 MET cc_start: 0.6145 (OUTLIER) cc_final: 0.4998 (ttm)
REVERT: A  343 ILE cc_start: 0.8452 (mt) cc_final: 0.8108 (mp)
REVERT: B   96 ARG cc_start: 0.8292 (mtt180) cc_final: 0.7991 (mtt180)
REVERT: B  263 THR cc_start: 0.8551 (t) cc_final: 0.8095 (m)
REVERT: R   78 ILE cc_start: 0.6907 (pp) cc_final: 0.6665 (tt)
REVERT: R  121 TYR cc_start: 0.7566 (t80) cc_final: 0.7019 (t80)
REVERT: R  305 ILE cc_start: 0.6965 (mt) cc_final: 0.6757 (mp)
  outliers start: 21
  outliers final: 13
  residues processed: 111
  average time/residue: 0.4799
  time to fit residues: 56.8586
Evaluate side-chains
  108 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain R residue   96 VAL
Chi-restraints excluded: chain R residue  154 VAL
Chi-restraints excluded: chain R residue  172 CYS
Chi-restraints excluded: chain R residue  190 ILE
Chi-restraints excluded: chain R residue  272 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 70 optimal weight:    7.9990
   chunk 39 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0770
   chunk 76 optimal weight:    0.6980
   chunk 44 optimal weight:    0.0980
   chunk 17 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.4538

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
B 156 GLN
B 293 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.225478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.182667 restraints weight = 7488.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.4173 rms_B_bonded: 1.83
r_work: 0.3982 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3872 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.2826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7010  Z= 0.122
  Angle     :  0.523   7.673   9542  Z= 0.276
  Chirality :  0.041   0.143   1127
  Planarity :  0.003   0.034   1178
  Dihedral  :  6.485  54.364   1020
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 19.30 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (0.29), residues: 893
  helix:  2.00 (0.26), residues: 403
  sheet:  0.23 (0.37), residues: 177
  loop : -0.65 (0.36), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 134 
 TYR   0.009   0.001   TYR A 320 
 PHE   0.019   0.001   PHE R 195 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 7009)
  covalent geometry    : angle       0.52303 ( 9540)
  SS BOND              : bond        0.00148 (    1)
  SS BOND              : angle       0.95056 (    2)
  hydrogen bonds       : bond        0.03602 (  407)
  hydrogen bonds       : angle       4.37595 ( 1170)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A  188 HIS cc_start: 0.8024 (m90) cc_final: 0.7709 (m90)
REVERT: A  197 LYS cc_start: 0.8627 (mtmt) cc_final: 0.8321 (mmtp)
REVERT: A  216 GLU cc_start: 0.8104 (tt0) cc_final: 0.7901 (tt0)
REVERT: A  240 MET cc_start: 0.6083 (OUTLIER) cc_final: 0.4903 (ttm)
REVERT: A  343 ILE cc_start: 0.8380 (mt) cc_final: 0.8102 (mp)
REVERT: B   96 ARG cc_start: 0.8279 (mtt180) cc_final: 0.7977 (mtt180)
REVERT: R   78 ILE cc_start: 0.6914 (pp) cc_final: 0.6693 (tt)
REVERT: R  121 TYR cc_start: 0.7536 (t80) cc_final: 0.7004 (t80)
  outliers start: 22
  outliers final: 15
  residues processed: 106
  average time/residue: 0.4160
  time to fit residues: 47.4952
Evaluate side-chains
  109 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain R residue   96 VAL
Chi-restraints excluded: chain R residue  154 VAL
Chi-restraints excluded: chain R residue  172 CYS
Chi-restraints excluded: chain R residue  190 ILE
Chi-restraints excluded: chain R residue  272 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 4 optimal weight:    0.0570
   chunk 46 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   chunk 24 optimal weight:    0.2980
   chunk 55 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
B 293 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 260 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.225388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.182362 restraints weight = 7508.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.4172 rms_B_bonded: 1.76
r_work: 0.3974 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3862 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7010  Z= 0.125
  Angle     :  0.538   8.350   9542  Z= 0.281
  Chirality :  0.041   0.145   1127
  Planarity :  0.003   0.033   1178
  Dihedral  :  6.436  54.732   1020
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 19.88 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (0.29), residues: 893
  helix:  2.02 (0.26), residues: 403
  sheet:  0.21 (0.37), residues: 177
  loop : -0.66 (0.36), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 134 
 TYR   0.008   0.001   TYR R 137 
 PHE   0.024   0.001   PHE R 236 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.008   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 7009)
  covalent geometry    : angle       0.53785 ( 9540)
  SS BOND              : bond        0.00180 (    1)
  SS BOND              : angle       0.96515 (    2)
  hydrogen bonds       : bond        0.03577 (  407)
  hydrogen bonds       : angle       4.37109 ( 1170)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A  197 LYS cc_start: 0.8631 (mtmt) cc_final: 0.8315 (mmtp)
REVERT: A  240 MET cc_start: 0.6058 (OUTLIER) cc_final: 0.4865 (ttm)
REVERT: A  343 ILE cc_start: 0.8387 (mt) cc_final: 0.8137 (mp)
REVERT: B   96 ARG cc_start: 0.8283 (mtt180) cc_final: 0.8038 (mtt180)
REVERT: R   78 ILE cc_start: 0.7285 (pp) cc_final: 0.7076 (tt)
REVERT: R  121 TYR cc_start: 0.7568 (t80) cc_final: 0.7057 (t80)
REVERT: R  122 LYS cc_start: 0.7842 (mtpp) cc_final: 0.7332 (mtpt)
  outliers start: 19
  outliers final: 14
  residues processed: 109
  average time/residue: 0.4215
  time to fit residues: 49.2097
Evaluate side-chains
  109 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain R residue   96 VAL
Chi-restraints excluded: chain R residue  154 VAL
Chi-restraints excluded: chain R residue  172 CYS
Chi-restraints excluded: chain R residue  190 ILE
Chi-restraints excluded: chain R residue  272 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0670
   chunk 72 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 87 optimal weight:    5.9990
   chunk 17 optimal weight:    0.0970
   chunk 58 optimal weight:    0.1980
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.4316

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4618 r_free = 0.4618 target = 0.225681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.182725 restraints weight = 7460.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.4175 rms_B_bonded: 1.71
r_work: 0.3987 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3877 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.2955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7010  Z= 0.121
  Angle     :  0.538   7.619   9542  Z= 0.280
  Chirality :  0.041   0.234   1127
  Planarity :  0.003   0.034   1178
  Dihedral  :  6.401  55.974   1020
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 19.45 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.29), residues: 893
  helix:  2.05 (0.26), residues: 404
  sheet:  0.19 (0.37), residues: 177
  loop : -0.66 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 134 
 TYR   0.009   0.001   TYR R  49 
 PHE   0.019   0.001   PHE R 195 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.009   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 7009)
  covalent geometry    : angle       0.53797 ( 9540)
  SS BOND              : bond        0.00120 (    1)
  SS BOND              : angle       0.99960 (    2)
  hydrogen bonds       : bond        0.03558 (  407)
  hydrogen bonds       : angle       4.37433 ( 1170)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  197 LYS cc_start: 0.8618 (mtmt) cc_final: 0.8310 (mmtp)
REVERT: A  240 MET cc_start: 0.6027 (OUTLIER) cc_final: 0.4850 (ttm)
REVERT: A  343 ILE cc_start: 0.8334 (mt) cc_final: 0.8088 (mp)
REVERT: B   96 ARG cc_start: 0.8246 (mtt180) cc_final: 0.7974 (mtt180)
REVERT: R   78 ILE cc_start: 0.7248 (pp) cc_final: 0.7035 (tt)
REVERT: R  121 TYR cc_start: 0.7560 (t80) cc_final: 0.7057 (t80)
REVERT: R  122 LYS cc_start: 0.7849 (mtpp) cc_final: 0.7321 (mtpt)
  outliers start: 16
  outliers final: 13
  residues processed: 106
  average time/residue: 0.4145
  time to fit residues: 47.3202
Evaluate side-chains
  106 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain R residue   96 VAL
Chi-restraints excluded: chain R residue  154 VAL
Chi-restraints excluded: chain R residue  172 CYS
Chi-restraints excluded: chain R residue  190 ILE
Chi-restraints excluded: chain R residue  272 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 9 optimal weight:    0.4980
   chunk 29 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   chunk 85 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 260 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.224394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.181085 restraints weight = 7430.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.4157 rms_B_bonded: 1.69
r_work: 0.3959 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3848 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7010  Z= 0.142
  Angle     :  0.556   7.833   9542  Z= 0.290
  Chirality :  0.042   0.228   1127
  Planarity :  0.003   0.033   1178
  Dihedral  :  6.428  55.620   1020
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 19.59 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.29), residues: 893
  helix:  2.01 (0.26), residues: 404
  sheet:  0.17 (0.37), residues: 177
  loop : -0.68 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 134 
 TYR   0.018   0.001   TYR R  29 
 PHE   0.024   0.002   PHE R 236 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.010   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 7009)
  covalent geometry    : angle       0.55634 ( 9540)
  SS BOND              : bond        0.00065 (    1)
  SS BOND              : angle       0.88099 (    2)
  hydrogen bonds       : bond        0.03659 (  407)
  hydrogen bonds       : angle       4.43074 ( 1170)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2914.56 seconds
wall clock time: 50 minutes 39.42 seconds (3039.42 seconds total)