Starting phenix.real_space_refine
on Wed Mar 12 05:07:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x9c_33071/03_2025/7x9c_33071.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x9c_33071/03_2025/7x9c_33071.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x9c_33071/03_2025/7x9c_33071.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x9c_33071/03_2025/7x9c_33071.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x9c_33071/03_2025/7x9c_33071.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x9c_33071/03_2025/7x9c_33071.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 139 atoms to isotropic.
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      62      5.16       5
     C    4615      2.51       5
     N    1240      2.21       5
     O    1302      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7219
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 2358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2358
          Classifications: {'peptide': 302}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 9, 'TRANS': 292}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "A"
      Number of atoms: 1691
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1691
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 51
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 34
    Chain: "B"
      Number of atoms: 2503
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2503
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 81
          Unresolved non-hydrogen angles: 99
          Unresolved non-hydrogen dihedrals: 63
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 71
    Chain: "C"
      Number of atoms: 383
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 383
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 29
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 24
    Chain: "P"
      Number of atoms: 284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 284
          Classifications: {'peptide': 36}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 30}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 10
  Time building chain proxies: 5.14, per 1000 atoms: 0.71
  Number of scatterers: 7219
  At special positions: 0
  Unit cell: (123.31, 119.13, 84.645, 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      62     16.00
     O    1302      8.00
     N    1240      7.00
     C    4615      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 114 " - pdb=" SG  CYS R 201 " 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: 1.86
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1798

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 8 sheets defined
      47.1% alpha, 16.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'R' and resid 38 through 68
      removed outlier: 3.955A  pdb=" N   VAL R  42 " --> pdb=" O   VAL R  38 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 74 through 103
      removed outlier: 3.908A  pdb=" N   LEU R  78 " --> pdb=" O   ASN R  74 " (cutoff:3.500A)
      Proline residue:  R  96  - end of helix
    Processing helix  chain 'R' and resid 110 through 144
    Processing helix  chain 'R' and resid 152 through 172
    Processing helix  chain 'R' and resid 172 through 177
      removed outlier: 3.612A  pdb=" N   ALA R 176 " --> pdb=" O   LEU R 172 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 207 through 223
      removed outlier: 3.898A  pdb=" N   ILE R 213 " --> pdb=" O   HIS R 209 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   TYR R 214 " --> pdb=" O   HIS R 210 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   THR R 215 " --> pdb=" O   ARG R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 223 through 248
      removed outlier: 3.580A  pdb=" N   VAL R 247 " --> pdb=" O   ARG R 243 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 257 through 277
    Processing helix  chain 'R' and resid 278 through 291
      removed outlier: 3.746A  pdb=" N   HIS R 282 " --> pdb=" O   TRP R 278 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 299 through 313
    Processing helix  chain 'R' and resid 313 through 323
      Proline residue:  R 319  - end of helix
    Processing helix  chain 'R' and resid 326 through 330
      removed outlier: 3.671A  pdb=" N   LYS R 330 " --> pdb=" O   THR R 327 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 331 through 341
      removed outlier: 3.663A  pdb=" N   ALA R 335 " --> pdb=" O   LYS R 331 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   VAL R 337 " --> pdb=" O   ILE R 333 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LEU R 338 " --> pdb=" O   LYS R 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 33
    Processing helix  chain 'A' and resid 45 through 51
      removed outlier: 3.628A  pdb=" N   LYS A  51 " --> pdb=" O   CYS A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.080A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
      removed outlier: 3.822A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 213 through 216'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 4.203A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 279
      removed outlier: 3.634A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.515A  pdb=" N   PHE A 307 " --> pdb=" O   ILE A 303 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLU A 308 " --> pdb=" O   GLN A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 352
      removed outlier: 3.786A  pdb=" N   PHE A 334 " --> pdb=" O   LYS A 330 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 26
      removed outlier: 3.653A  pdb=" N   GLU B  10 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ASN B  16 " --> pdb=" O   GLU B  12 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   GLN B  17 " --> pdb=" O   GLN B  13 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ILE B  18 " --> pdb=" O   LEU B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 128 through 132
      removed outlier: 3.841A  pdb=" N   GLY B 131 " --> pdb=" O   THR B 128 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ASN B 132 " --> pdb=" O   ARG B 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 128 through 132'
    Processing helix  chain 'B' and resid 280 through 282
      No H-bonds generated for 'chain 'B' and resid 280 through 282'
    Processing helix  chain 'C' and resid 10 through 20
      removed outlier: 3.812A  pdb=" N   LYS C  14 " --> pdb=" O   ALA C  10 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 20 through 25
      removed outlier: 3.575A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'P' and resid 13 through 32
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.885A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.268A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.470A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.715A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 5.458A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ILE B  81 " --> pdb=" O   HIS B  91 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.890A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.385A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.663A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.824A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191
      removed outlier: 7.105A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.548A  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 232
      removed outlier: 7.096A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 7.425A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278

    371 hydrogen bonds defined for protein.
    1074 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: 2.20

  Time building geometry restraints manager: 2.23 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1161
        1.31 -     1.43: 1987
        1.43 -     1.56: 4130
        1.56 -     1.69: 1
        1.69 -     1.81: 87
  Bond restraints: 7366
  Sorted by residual:
  bond pdb=" C   TYC P  36 "
       pdb=" NXT TYC P  36 "
    ideal  model  delta    sigma   weight residual
    1.340  1.449 -0.109 2.00e-02 2.50e+03 2.98e+01
  bond pdb=" CA  LYS R 190 "
       pdb=" C   LYS R 190 "
    ideal  model  delta    sigma   weight residual
    1.522  1.583 -0.060 1.20e-02 6.94e+03 2.54e+01
  bond pdb=" N   LEU R 192 "
       pdb=" CA  LEU R 192 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.034 1.26e-02 6.30e+03 7.20e+00
  bond pdb=" N   GLN R 121 "
       pdb=" CA  GLN R 121 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.23e-02 6.61e+03 6.28e+00
  bond pdb=" CZ  TYC P  36 "
       pdb=" OH  TYC P  36 "
    ideal  model  delta    sigma   weight residual
    1.350  1.399 -0.049 2.00e-02 2.50e+03 6.09e+00
  ... (remaining 7361 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 9866
        1.68 -     3.36: 122
        3.36 -     5.03: 21
        5.03 -     6.71: 5
        6.71 -     8.39: 1
  Bond angle restraints: 10015
  Sorted by residual:
  angle pdb=" N   ILE B 270 "
        pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
      ideal   model   delta    sigma   weight residual
     113.47  109.46    4.01 1.01e+00 9.80e-01 1.58e+01
  angle pdb=" C   GLN R 121 "
        pdb=" CA  GLN R 121 "
        pdb=" CB  GLN R 121 "
      ideal   model   delta    sigma   weight residual
     110.85  115.85   -5.00 1.70e+00 3.46e-01 8.65e+00
  angle pdb=" C   ILE R 144 "
        pdb=" N   ASN R 145 "
        pdb=" CA  ASN R 145 "
      ideal   model   delta    sigma   weight residual
     121.80  128.47   -6.67 2.44e+00 1.68e-01 7.48e+00
  angle pdb=" CA  LEU R 172 "
        pdb=" CB  LEU R 172 "
        pdb=" CG  LEU R 172 "
      ideal   model   delta    sigma   weight residual
     116.30  124.69   -8.39 3.50e+00 8.16e-02 5.75e+00
  angle pdb=" CA  GLN R 121 "
        pdb=" C   GLN R 121 "
        pdb=" O   GLN R 121 "
      ideal   model   delta    sigma   weight residual
     120.42  117.91    2.51 1.06e+00 8.90e-01 5.61e+00
  ... (remaining 10010 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.95: 4097
       15.95 -    31.89: 212
       31.89 -    47.84: 46
       47.84 -    63.78: 8
       63.78 -    79.73: 1
  Dihedral angle restraints: 4364
    sinusoidal: 1602
      harmonic: 2762
  Sorted by residual:
  dihedral pdb=" CA  TYR B  85 "
           pdb=" C   TYR B  85 "
           pdb=" N   THR B  86 "
           pdb=" CA  THR B  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.68   15.32     0      5.00e+00 4.00e-02 9.39e+00
  dihedral pdb=" C   GLN R 121 "
           pdb=" N   GLN R 121 "
           pdb=" CA  GLN R 121 "
           pdb=" CB  GLN R 121 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.21    7.61     0      2.50e+00 1.60e-01 9.27e+00
  dihedral pdb=" CB  GLU R 181 "
           pdb=" CG  GLU R 181 "
           pdb=" CD  GLU R 181 "
           pdb=" OE1 GLU R 181 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   79.73  -79.73     1      3.00e+01 1.11e-03 8.76e+00
  ... (remaining 4361 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 848
       0.037 -    0.073: 257
       0.073 -    0.110: 61
       0.110 -    0.147: 15
       0.147 -    0.183: 1
  Chirality restraints: 1182
  Sorted by residual:
  chirality pdb=" CA  GLN R 121 "
            pdb=" N   GLN R 121 "
            pdb=" C   GLN R 121 "
            pdb=" CB  GLN R 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.39e-01
  chirality pdb=" CA  VAL B 327 "
            pdb=" N   VAL B 327 "
            pdb=" C   VAL B 327 "
            pdb=" CB  VAL B 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.99e-01
  chirality pdb=" CA  HIS R 188 "
            pdb=" N   HIS R 188 "
            pdb=" C   HIS R 188 "
            pdb=" CB  HIS R 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.87e-01
  ... (remaining 1179 not shown)

  Planarity restraints: 1260
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 225 "   -0.021 5.00e-02 4.00e+02   3.11e-02 1.54e+00
        pdb=" N   PRO R 226 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO R 226 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO R 226 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 172 "   -0.019 5.00e-02 4.00e+02   2.85e-02 1.30e+00
        pdb=" N   PRO R 173 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO R 173 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO R 173 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "    0.017 5.00e-02 4.00e+02   2.61e-02 1.09e+00
        pdb=" N   PRO B 194 "   -0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1257 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 734
        2.75 -     3.28: 7402
        3.28 -     3.82: 12388
        3.82 -     4.36: 14451
        4.36 -     4.90: 24900
  Nonbonded interactions: 59875
  Sorted by model distance:
  nonbonded pdb=" OH  TYR R  48 "
            pdb=" O   LEU R 305 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OG1 THR B 128 "
            pdb=" O   ASN B 132 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" OG1 THR B 184 "
            pdb=" OD2 ASP B 205 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OH  TYR A 290 "
            pdb=" OE1 GLU A 298 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" OG1 THR R  52 "
            pdb=" OE1 GLN R  95 "
     model   vdw
     2.329 3.040
  ... (remaining 59870 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:             1.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     22.700
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:42.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   67.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6837
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      :  0.003   0.109   7366  Z= 0.197
  Angle     :  0.510   8.390  10015  Z= 0.287
  Chirality :  0.038   0.183   1182
  Planarity :  0.003   0.031   1260
  Dihedral  : 10.402  79.725   2563
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.24), residues: 928
  helix: -1.03 (0.24), residues: 392
  sheet: -1.64 (0.36), residues: 183
  loop : -2.20 (0.28), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 205 
 HIS   0.005   0.000   HIS R 188 
 PHE   0.010   0.001   PHE B 253 
 TYR   0.014   0.001   TYR R  48 
 ARG   0.001   0.000   ARG B  52 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
REVERT: R  109 PHE cc_start: 0.7654 (m-80) cc_final: 0.7426 (m-80)
REVERT: R  115 LYS cc_start: 0.5513 (mtpp) cc_final: 0.5241 (mmpt)
REVERT: A   35 LYS cc_start: 0.8108 (mtmm) cc_final: 0.7903 (mtmm)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 1.2104
  time to fit residues: 206.9246
Evaluate side-chains
  112 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0770
   chunk 37 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 53 optimal weight:    9.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.7140

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
A 306 GLN
A 322 HIS
B 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.179292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.132876 restraints weight = 8009.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 2.52
r_work: 0.3470 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7366  Z= 0.222
  Angle     :  0.582   9.128  10015  Z= 0.299
  Chirality :  0.041   0.140   1182
  Planarity :  0.003   0.028   1260
  Dihedral  :  5.247  59.245   1013
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 11.42 %
    Favored  : 86.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.26), residues: 928
  helix:  0.18 (0.26), residues: 407
  sheet: -1.33 (0.36), residues: 178
  loop : -1.89 (0.30), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 185 
 PHE   0.013   0.001   PHE A 274 
 TYR   0.014   0.002   TYR R 234 
 ARG   0.004   0.000   ARG B  22 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 1.111 
Fit side-chains
   revert: symmetry clash
REVERT: R  109 PHE cc_start: 0.7935 (m-80) cc_final: 0.7682 (m-80)
REVERT: R  115 LYS cc_start: 0.5525 (mtpp) cc_final: 0.5020 (mmpt)
REVERT: A   35 LYS cc_start: 0.8410 (mtmm) cc_final: 0.8066 (mtmm)
REVERT: A  198 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7258 (mpt)
REVERT: A  258 TRP cc_start: 0.8069 (m-90) cc_final: 0.7728 (m-10)
REVERT: B  259 GLN cc_start: 0.7416 (tp40) cc_final: 0.7067 (tp40)
REVERT: B  262 MET cc_start: 0.7677 (ttm) cc_final: 0.7450 (mtm)
  outliers start: 16
  outliers final: 8
  residues processed: 134
  average time/residue: 1.1927
  time to fit residues: 169.9180
Evaluate side-chains
  120 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  219 LEU
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain P residue   31 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 65 optimal weight:    0.4980
   chunk 41 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 83 optimal weight:    0.3980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
R 185 HIS
B 220 GLN
B 230 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.175667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.134898 restraints weight = 8108.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 2.28
r_work: 0.3444 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
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      :  0.003   0.027   7366  Z= 0.201
  Angle     :  0.553  10.224  10015  Z= 0.281
  Chirality :  0.040   0.129   1182
  Planarity :  0.003   0.028   1260
  Dihedral  :  5.225  58.579   1013
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 13.68 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.27), residues: 928
  helix:  0.60 (0.26), residues: 415
  sheet: -1.12 (0.37), residues: 171
  loop : -1.78 (0.31), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.022   0.001   PHE R 284 
 TYR   0.020   0.001   TYR A 230 
 ARG   0.003   0.000   ARG B 256 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 126
  time to evaluate  : 0.827 
Fit side-chains
REVERT: R  109 PHE cc_start: 0.7949 (m-80) cc_final: 0.7681 (m-80)
REVERT: R  115 LYS cc_start: 0.5273 (mtpp) cc_final: 0.4745 (mmpt)
REVERT: R  260 MET cc_start: 0.6114 (mmp) cc_final: 0.5833 (tpp)
REVERT: A   22 ASN cc_start: 0.8085 (m110) cc_final: 0.7848 (m110)
REVERT: A   35 LYS cc_start: 0.8371 (mtmm) cc_final: 0.8009 (mtmm)
REVERT: A  198 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7422 (mpt)
REVERT: A  258 TRP cc_start: 0.7944 (m-90) cc_final: 0.7739 (m-10)
REVERT: B  259 GLN cc_start: 0.7396 (tp40) cc_final: 0.7060 (tp40)
REVERT: P    4 GLU cc_start: 0.7064 (pm20) cc_final: 0.6779 (pt0)
  outliers start: 27
  outliers final: 12
  residues processed: 140
  average time/residue: 1.0141
  time to fit residues: 152.2848
Evaluate side-chains
  130 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 1.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  219 LEU
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain R residue  284 PHE
Chi-restraints excluded: chain R residue  327 THR
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain P residue   31 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   chunk 54 optimal weight:    0.0170
   chunk 91 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 42 optimal weight:    0.4980
   chunk 83 optimal weight:    0.9980
   overall best weight:    0.6620

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

Flipped N/Q/H residues before XYZ refinement:
R 185 HIS
R 222 GLN
B 125 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.173913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.130176 restraints weight = 8085.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 2.51
r_work: 0.3387 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.2973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7366  Z= 0.207
  Angle     :  0.567  10.599  10015  Z= 0.285
  Chirality :  0.040   0.144   1182
  Planarity :  0.003   0.029   1260
  Dihedral  :  5.327  58.883   1013
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 16.20 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.27), residues: 928
  helix:  0.88 (0.26), residues: 414
  sheet: -1.06 (0.37), residues: 171
  loop : -1.64 (0.31), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.012   0.001   PHE B 253 
 TYR   0.022   0.001   TYR A 230 
 ARG   0.002   0.000   ARG B 256 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.911 
Fit side-chains
REVERT: R  104 MET cc_start: 0.4082 (ptp) cc_final: 0.3812 (pp-130)
REVERT: R  115 LYS cc_start: 0.5283 (mtpp) cc_final: 0.4752 (mmpt)
REVERT: R  185 HIS cc_start: 0.6710 (OUTLIER) cc_final: 0.6072 (m90)
REVERT: R  260 MET cc_start: 0.6259 (mmp) cc_final: 0.6000 (tpp)
REVERT: R  327 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7589 (m)
REVERT: A   22 ASN cc_start: 0.8029 (m110) cc_final: 0.7815 (m110)
REVERT: A   28 GLU cc_start: 0.7528 (pt0) cc_final: 0.7304 (pt0)
REVERT: A  197 LYS cc_start: 0.8570 (mtmt) cc_final: 0.8324 (mtpp)
REVERT: A  198 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7569 (mpt)
REVERT: B  127 LYS cc_start: 0.7924 (mmtp) cc_final: 0.7258 (mmtp)
REVERT: B  259 GLN cc_start: 0.7487 (tp40) cc_final: 0.7144 (tp40)
REVERT: B  336 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8206 (tt)
  outliers start: 20
  outliers final: 11
  residues processed: 124
  average time/residue: 1.4017
  time to fit residues: 186.2020
Evaluate side-chains
  126 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  185 HIS
Chi-restraints excluded: chain R residue  219 LEU
Chi-restraints excluded: chain R residue  272 VAL
Chi-restraints excluded: chain R residue  327 THR
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain P residue   31 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 88 optimal weight:    0.4980
   chunk 2 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
R 145 ASN
R 185 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.171173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.126880 restraints weight = 8014.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 2.62
r_work: 0.3367 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7366  Z= 0.238
  Angle     :  0.580  11.109  10015  Z= 0.292
  Chirality :  0.041   0.125   1182
  Planarity :  0.003   0.029   1260
  Dihedral  :  5.417  59.967   1013
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 16.20 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.27), residues: 928
  helix:  1.01 (0.26), residues: 414
  sheet: -1.19 (0.36), residues: 178
  loop : -1.51 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 258 
 HIS   0.016   0.001   HIS R 185 
 PHE   0.018   0.002   PHE R 284 
 TYR   0.023   0.001   TYR A 230 
 ARG   0.003   0.000   ARG B 314 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 119
  time to evaluate  : 0.794 
Fit side-chains
   revert: symmetry clash
REVERT: R  104 MET cc_start: 0.4280 (ptp) cc_final: 0.3928 (pp-130)
REVERT: R  115 LYS cc_start: 0.5259 (mtpp) cc_final: 0.4699 (mmpt)
REVERT: R  260 MET cc_start: 0.6211 (mmp) cc_final: 0.6004 (tpp)
REVERT: R  327 THR cc_start: 0.8105 (OUTLIER) cc_final: 0.7781 (m)
REVERT: A   22 ASN cc_start: 0.7984 (m110) cc_final: 0.7764 (m110)
REVERT: A   28 GLU cc_start: 0.7468 (pt0) cc_final: 0.7243 (pt0)
REVERT: A  198 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7591 (mpt)
REVERT: B  258 ASP cc_start: 0.7113 (t0) cc_final: 0.6876 (t0)
REVERT: B  259 GLN cc_start: 0.7633 (tp40) cc_final: 0.7297 (tp40)
REVERT: B  336 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8272 (tt)
  outliers start: 27
  outliers final: 11
  residues processed: 135
  average time/residue: 1.0693
  time to fit residues: 153.8945
Evaluate side-chains
  129 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  219 LEU
Chi-restraints excluded: chain R residue  272 VAL
Chi-restraints excluded: chain R residue  327 THR
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain P residue   31 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 85 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
R 145 ASN
R 185 HIS
R 222 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.169420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.126712 restraints weight = 8095.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 2.43
r_work: 0.3331 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.3675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7366  Z= 0.258
  Angle     :  0.604  11.420  10015  Z= 0.304
  Chirality :  0.041   0.131   1182
  Planarity :  0.003   0.030   1260
  Dihedral  :  5.419  58.057   1013
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 17.66 %
    Favored  : 78.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.27), residues: 928
  helix:  1.16 (0.26), residues: 406
  sheet: -1.29 (0.35), residues: 179
  loop : -1.40 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 258 
 HIS   0.005   0.001   HIS R 185 
 PHE   0.015   0.001   PHE B 253 
 TYR   0.022   0.002   TYR A 230 
 ARG   0.002   0.000   ARG A  32 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 115
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
REVERT: R  115 LYS cc_start: 0.5165 (mtpp) cc_final: 0.4583 (mmpt)
REVERT: R  185 HIS cc_start: 0.6617 (OUTLIER) cc_final: 0.6203 (m-70)
REVERT: R  260 MET cc_start: 0.6448 (mmp) cc_final: 0.6175 (tpp)
REVERT: R  327 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7903 (m)
REVERT: A   22 ASN cc_start: 0.8002 (m110) cc_final: 0.7773 (m110)
REVERT: A   28 GLU cc_start: 0.7522 (pt0) cc_final: 0.7295 (pt0)
REVERT: A  198 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7617 (mpt)
REVERT: B  259 GLN cc_start: 0.7788 (tp40) cc_final: 0.7447 (tp40)
REVERT: B  336 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8346 (tt)
  outliers start: 29
  outliers final: 14
  residues processed: 132
  average time/residue: 0.9641
  time to fit residues: 136.4195
Evaluate side-chains
  130 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   88 PHE
Chi-restraints excluded: chain R residue  185 HIS
Chi-restraints excluded: chain R residue  213 ILE
Chi-restraints excluded: chain R residue  219 LEU
Chi-restraints excluded: chain R residue  272 VAL
Chi-restraints excluded: chain R residue  327 THR
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain P residue   31 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0980
   chunk 13 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 90 optimal weight:    9.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
R 145 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.170828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.126724 restraints weight = 8009.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 2.44
r_work: 0.3367 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.3742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7366  Z= 0.213
  Angle     :  0.602  11.521  10015  Z= 0.301
  Chirality :  0.041   0.134   1182
  Planarity :  0.003   0.031   1260
  Dihedral  :  5.329  56.952   1013
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 18.99 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.27), residues: 928
  helix:  1.23 (0.27), residues: 406
  sheet: -1.17 (0.35), residues: 177
  loop : -1.36 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 107 
 HIS   0.012   0.001   HIS R 185 
 PHE   0.014   0.001   PHE B 253 
 TYR   0.020   0.001   TYR A 230 
 ARG   0.002   0.000   ARG A  32 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 116
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
REVERT: R  260 MET cc_start: 0.6324 (mmp) cc_final: 0.6104 (tpp)
REVERT: R  327 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7889 (m)
REVERT: A   22 ASN cc_start: 0.8017 (m110) cc_final: 0.7780 (m110)
REVERT: A   28 GLU cc_start: 0.7508 (pt0) cc_final: 0.7265 (pt0)
REVERT: A  198 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7475 (mpt)
REVERT: B  145 TYR cc_start: 0.8854 (p90) cc_final: 0.8412 (p90)
REVERT: B  259 GLN cc_start: 0.7741 (tp40) cc_final: 0.7439 (tp40)
REVERT: B  336 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8291 (tt)
  outliers start: 26
  outliers final: 15
  residues processed: 132
  average time/residue: 0.9005
  time to fit residues: 127.5100
Evaluate side-chains
  130 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  213 ILE
Chi-restraints excluded: chain R residue  219 LEU
Chi-restraints excluded: chain R residue  272 VAL
Chi-restraints excluded: chain R residue  327 THR
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   46 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 53 optimal weight:   20.0000
   chunk 52 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 17 optimal weight:    6.9990
   chunk 78 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 28 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
R 145 ASN
R 222 GLN
R 264 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.166071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.122628 restraints weight = 8160.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 2.48
r_work: 0.3296 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.4138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   7366  Z= 0.308
  Angle     :  0.653  11.606  10015  Z= 0.329
  Chirality :  0.043   0.162   1182
  Planarity :  0.003   0.033   1260
  Dihedral  :  5.556  56.486   1013
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 20.19 %
    Favored  : 76.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.27), residues: 928
  helix:  1.13 (0.26), residues: 403
  sheet: -1.23 (0.37), residues: 174
  loop : -1.32 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 258 
 HIS   0.006   0.001   HIS B 142 
 PHE   0.015   0.002   PHE B 253 
 TYR   0.021   0.002   TYR B  59 
 ARG   0.003   0.000   ARG P  35 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.857 
Fit side-chains
   revert: symmetry clash
REVERT: R  327 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8069 (m)
REVERT: A   14 GLU cc_start: 0.7632 (tp30) cc_final: 0.7422 (tp30)
REVERT: A   22 ASN cc_start: 0.8119 (m110) cc_final: 0.7881 (m110)
REVERT: A   28 GLU cc_start: 0.7521 (pt0) cc_final: 0.7286 (pt0)
REVERT: A  198 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7612 (mpt)
REVERT: A  209 LYS cc_start: 0.9136 (pttm) cc_final: 0.8901 (pttp)
REVERT: B  259 GLN cc_start: 0.7930 (tp40) cc_final: 0.7553 (tp40)
  outliers start: 25
  outliers final: 13
  residues processed: 133
  average time/residue: 1.0244
  time to fit residues: 145.2844
Evaluate side-chains
  129 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  213 ILE
Chi-restraints excluded: chain R residue  219 LEU
Chi-restraints excluded: chain R residue  272 VAL
Chi-restraints excluded: chain R residue  327 THR
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain C residue   46 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 54 optimal weight:    0.4980
   chunk 64 optimal weight:    0.2980
   chunk 16 optimal weight:    4.9990
   chunk 53 optimal weight:    9.9990
   chunk 83 optimal weight:    0.0670
   chunk 70 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 84 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 88 optimal weight:    0.6980
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
R 145 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.170927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.128198 restraints weight = 8112.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 2.44
r_work: 0.3360 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.4065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7366  Z= 0.195
  Angle     :  0.621  11.278  10015  Z= 0.310
  Chirality :  0.041   0.156   1182
  Planarity :  0.003   0.033   1260
  Dihedral  :  5.443  58.708   1013
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 21.78 %
    Favored  : 75.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.27), residues: 928
  helix:  1.26 (0.27), residues: 403
  sheet: -1.23 (0.37), residues: 162
  loop : -1.33 (0.30), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R 107 
 HIS   0.003   0.001   HIS R 188 
 PHE   0.015   0.001   PHE R  88 
 TYR   0.017   0.001   TYR A 230 
 ARG   0.003   0.000   ARG A 205 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  327 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7887 (m)
REVERT: A  198 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7521 (mpt)
REVERT: A  209 LYS cc_start: 0.9109 (pttm) cc_final: 0.8884 (pttp)
REVERT: B  145 TYR cc_start: 0.8808 (p90) cc_final: 0.8307 (p90)
REVERT: B  259 GLN cc_start: 0.7840 (tp40) cc_final: 0.7587 (tp40)
  outliers start: 21
  outliers final: 14
  residues processed: 134
  average time/residue: 0.9722
  time to fit residues: 139.1691
Evaluate side-chains
  128 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  205 TRP
Chi-restraints excluded: chain R residue  213 ILE
Chi-restraints excluded: chain R residue  219 LEU
Chi-restraints excluded: chain R residue  272 VAL
Chi-restraints excluded: chain R residue  327 THR
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain C residue   46 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 29 optimal weight:    8.9990
   chunk 68 optimal weight:    1.9990
   chunk 43 optimal weight:    0.4980
   chunk 90 optimal weight:   20.0000
   chunk 36 optimal weight:    0.7980
   chunk 78 optimal weight:    0.8980
   chunk 86 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 63 optimal weight:    0.0020
   chunk 73 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
R 145 ASN
R 222 GLN
B 239 ASN
B 259 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.170154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.129155 restraints weight = 8268.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 2.38
r_work: 0.3369 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.4144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7366  Z= 0.220
  Angle     :  0.647  11.277  10015  Z= 0.325
  Chirality :  0.042   0.161   1182
  Planarity :  0.003   0.035   1260
  Dihedral  :  5.451  59.158   1013
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 22.44 %
    Favored  : 75.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.28), residues: 928
  helix:  1.31 (0.27), residues: 404
  sheet: -1.18 (0.38), residues: 162
  loop : -1.28 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 107 
 HIS   0.004   0.001   HIS R 188 
 PHE   0.014   0.001   PHE B 253 
 TYR   0.016   0.001   TYR A 230 
 ARG   0.003   0.000   ARG R 211 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  327 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7893 (m)
REVERT: A   22 ASN cc_start: 0.8142 (m-40) cc_final: 0.7897 (m110)
REVERT: A  198 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7535 (mpt)
REVERT: A  209 LYS cc_start: 0.9056 (pttm) cc_final: 0.8855 (pttp)
REVERT: B  145 TYR cc_start: 0.8811 (p90) cc_final: 0.8277 (p90)
REVERT: B  325 MET cc_start: 0.7309 (tpp) cc_final: 0.7053 (tpp)
  outliers start: 15
  outliers final: 11
  residues processed: 125
  average time/residue: 1.0111
  time to fit residues: 134.8784
Evaluate side-chains
  124 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  205 TRP
Chi-restraints excluded: chain R residue  219 LEU
Chi-restraints excluded: chain R residue  272 VAL
Chi-restraints excluded: chain R residue  327 THR
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain C residue   46 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 85 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0870
   chunk 17 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.7360

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

Flipped N/Q/H residues before XYZ refinement:
R 145 ASN
B 239 ASN
B 259 GLN
B 266 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.169327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.125256 restraints weight = 8087.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 2.56
r_work: 0.3337 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.4213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7366  Z= 0.236
  Angle     :  0.647  11.184  10015  Z= 0.325
  Chirality :  0.042   0.160   1182
  Planarity :  0.003   0.035   1260
  Dihedral  :  5.487  58.759   1013
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 22.44 %
    Favored  : 75.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.28), residues: 928
  helix:  1.26 (0.26), residues: 405
  sheet: -1.15 (0.37), residues: 167
  loop : -1.26 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R 107 
 HIS   0.004   0.001   HIS R 188 
 PHE   0.013   0.001   PHE R  88 
 TYR   0.016   0.001   TYR A 230 
 ARG   0.003   0.000   ARG P  33 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5560.12 seconds
wall clock time: 99 minutes 57.63 seconds (5997.63 seconds total)