Starting phenix.real_space_refine
on Thu Feb 13 20:57:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tzo_41764/02_2025/8tzo_41764.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tzo_41764/02_2025/8tzo_41764.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tzo_41764/02_2025/8tzo_41764.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tzo_41764/02_2025/8tzo_41764.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tzo_41764/02_2025/8tzo_41764.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tzo_41764/02_2025/8tzo_41764.cif"
  }
  resolution = 3.1
  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=   0.004 sd=   0.077
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: 6
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     P       1      5.49       5
     S      73      5.16       5
     C    5627      2.51       5
     N    1450      2.21       5
     O    1585      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8737
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 2341
          Classifications: {'peptide': 301}
          Link IDs: {'PTRANS': 11, 'TRANS': 289}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4037
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 496, 4037
          Classifications: {'peptide': 496}
          Link IDs: {'PTRANS': 21, 'TRANS': 474}
    Chain: "C"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2218
          Classifications: {'peptide': 273}
          Link IDs: {'PTRANS': 11, 'TRANS': 261}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 83
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 83
          Unusual residues: {'BMA': 1, 'GLC': 1, 'MAN': 3, 'NAG': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 7
    Chain: "A"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'PAM': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PAM:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 40
          Unusual residues: {'POV': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 12
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.91, per 1000 atoms: 0.68
  Number of scatterers: 8737
  At special positions: 0
  Unit cell: (106.24, 118.69, 132.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      1     19.99
     S      73     16.00
     P       1     15.00
     O    1585      8.00
     N    1450      7.00
     C    5627      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  38 " - pdb=" SG  CYS A  52 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  73 " - pdb=" SG  CYS A  84 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 123 " - pdb=" SG  CYS A 131 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 152 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 214 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 202 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 278 " - pdb=" SG  CYS A 309 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 294 " - pdb=" SG  CYS A 304 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 308 " - pdb=" SG  CYS A 348 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 324 " - pdb=" SG  CYS A 339 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 326 " - pdb=" SG  CYS A 336 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 331 " - pdb=" SG  CYS A 332 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  50 " - pdb=" SG  CYS B  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 162 " - pdb=" SG  CYS B 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 105 " - pdb=" SG  CYS C 137 " 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=1, symmetry=0
  Links applied
    ALPHA1-2
      " MAN D   4 " - " MAN D   5 "
      " MAN D   5 " - " MAN D   6 "
    ALPHA1-3
      " BMA D   3 " - " MAN D   4 "
      " MAN D   6 " - " GLC D   7 "
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
    NAG-ASN
      " NAG D   1 " - " ASN A 295 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.42
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1982

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 11 sheets defined
      42.5% alpha, 21.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 55 through 77
      removed outlier: 4.407A  pdb=" N   ILE A  60 " --> pdb=" O   PRO A  56 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   VAL A  61 " --> pdb=" O   ASP A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 125
      removed outlier: 3.571A  pdb=" N   GLN A 125 " --> pdb=" O   ALA A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 151
    Processing helix  chain 'A' and resid 154 through 168
      removed outlier: 3.752A  pdb=" N   TYR A 158 " --> pdb=" O   ALA A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 171
      No H-bonds generated for 'chain 'A' and resid 169 through 171'
    Processing helix  chain 'A' and resid 175 through 195
    Processing helix  chain 'A' and resid 220 through 233
      removed outlier: 3.533A  pdb=" N   LEU A 224 " --> pdb=" O   GLN A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 308
      removed outlier: 3.566A  pdb=" N   CYS A 308 " --> pdb=" O   CYS A 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 35
      removed outlier: 3.649A  pdb=" N   GLY B  32 " --> pdb=" O   ALA B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 81
    Processing helix  chain 'B' and resid 169 through 173
    Processing helix  chain 'B' and resid 227 through 258
      Proline residue:  B 243  - end of helix
    Processing helix  chain 'B' and resid 264 through 282
      removed outlier: 3.563A  pdb=" N   ILE B 280 " --> pdb=" O   SER B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 288
    Processing helix  chain 'B' and resid 295 through 322
    Processing helix  chain 'B' and resid 331 through 334
    Processing helix  chain 'B' and resid 335 through 361
      Proline residue:  B 341  - end of helix
      removed outlier: 4.589A  pdb=" N   VAL B 359 " --> pdb=" O   CYS B 355 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLN B 360 " --> pdb=" O   GLU B 356 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU B 361 " --> pdb=" O   ARG B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 370
    Processing helix  chain 'B' and resid 371 through 412
      removed outlier: 4.251A  pdb=" N   SER B 412 " --> pdb=" O   SER B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 417
    Processing helix  chain 'B' and resid 418 through 456
    Processing helix  chain 'B' and resid 469 through 492
      removed outlier: 4.025A  pdb=" N   PHE B 474 " --> pdb=" O   ASN B 470 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 31 through 36
      removed outlier: 3.788A  pdb=" N   SER C  35 " --> pdb=" O   ASP C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 122
      removed outlier: 3.827A  pdb=" N   MET C 122 " --> pdb=" O   GLN C 119 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 200
    Processing helix  chain 'C' and resid 302 through 307
      removed outlier: 3.861A  pdb=" N   ILE C 305 " --> pdb=" O   ASP C 302 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   TYR C 306 " --> pdb=" O   PRO C 303 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 335 through 377
      removed outlier: 5.147A  pdb=" N   VAL C 349 " --> pdb=" O   GLU C 345 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   ALA C 352 " --> pdb=" O   GLY C 348 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   ALA C 353 " --> pdb=" O   VAL C 349 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LYS C 377 " --> pdb=" O   ASP C 373 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 202
    Processing sheet with id=AA2, first strand: chain 'A' and resid 251 through 254
      removed outlier: 4.640A  pdb=" N   PHE A 251 " --> pdb=" O   VAL A 241 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 293 through 294
      removed outlier: 3.956A  pdb=" N   TYR A 346 " --> pdb=" O   CYS A 294 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 324
    Processing sheet with id=AA5, first strand: chain 'B' and resid 40 through 46
      removed outlier: 3.963A  pdb=" N   GLU B 215 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   ASP B 117 " --> pdb=" O   LYS B 217 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   ILE B 219 " --> pdb=" O   GLN B 115 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   GLN B 115 " --> pdb=" O   ILE B 219 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   LEU B 221 " --> pdb=" O   ILE B 113 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ILE B 113 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   GLY B 223 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   LEU B 111 " --> pdb=" O   GLY B 223 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   MET B 110 " --> pdb=" O   GLU B 186 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   GLU B 186 " --> pdb=" O   MET B 110 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   PHE B 112 " --> pdb=" O   PHE B 184 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 74
      removed outlier: 4.538A  pdb=" N   LYS B  49 " --> pdb=" O   ILE B  74 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ARG B 200 " --> pdb=" O   ASP B 135 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   TYR B 140 " --> pdb=" O   GLU B 150 " (cutoff:3.500A)
      removed outlier: 5.614A  pdb=" N   GLU B 150 " --> pdb=" O   TYR B 140 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 459 through 462
    Processing sheet with id=AA8, first strand: chain 'C' and resid 21 through 25
      removed outlier: 3.503A  pdb=" N   PHE C 330 " --> pdb=" O   GLU C  25 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   THR C 325 " --> pdb=" O   THR C  68 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 21 through 25
      removed outlier: 3.503A  pdb=" N   PHE C 330 " --> pdb=" O   GLU C  25 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   PHE C 327 " --> pdb=" O   LYS C  98 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   LYS C  98 " --> pdb=" O   PHE C 327 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   ASN C 329 " --> pdb=" O   THR C  96 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   THR C  96 " --> pdb=" O   ASN C 329 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   TYR C 182 " --> pdb=" O   SER C 193 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   SER C 193 " --> pdb=" O   TYR C 182 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   VAL C 184 " --> pdb=" O   VAL C 191 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 37 through 39
      removed outlier: 5.314A  pdb=" N   GLY C 312 " --> pdb=" O   PHE C  81 " (cutoff:3.500A)
      removed outlier: 5.679A  pdb=" N   TRP C 319 " --> pdb=" O   GLY C 107 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 37 through 39
      removed outlier: 5.314A  pdb=" N   GLY C 312 " --> pdb=" O   PHE C  81 " (cutoff:3.500A)

    459 hydrogen bonds defined for protein.
    1287 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: 2.81

  Time building geometry restraints manager: 2.72 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: 1400
        1.31 -     1.44: 2525
        1.44 -     1.56: 4924
        1.56 -     1.69: 3
        1.69 -     1.82: 107
  Bond restraints: 8959
  Sorted by residual:
  bond pdb=" C31 POV B 601 "
       pdb=" O31 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.327  1.418 -0.091 2.00e-02 2.50e+03 2.08e+01
  bond pdb=" C21 POV B 601 "
       pdb=" O21 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.330  1.420 -0.090 2.00e-02 2.50e+03 2.00e+01
  bond pdb="C210 POV B 601 "
       pdb="C211 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.497  1.558 -0.061 2.00e-02 2.50e+03 9.16e+00
  bond pdb=" N   POV B 601 "
       pdb=" C14 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.490  1.435  0.055 2.00e-02 2.50e+03 7.59e+00
  bond pdb=" N   POV B 601 "
       pdb=" C12 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.508  1.455  0.053 2.00e-02 2.50e+03 6.95e+00
  ... (remaining 8954 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 11914
        2.49 -     4.99: 155
        4.99 -     7.48: 17
        7.48 -     9.97: 7
        9.97 -    12.47: 2
  Bond angle restraints: 12095
  Sorted by residual:
  angle pdb=" O11 POV B 601 "
        pdb=" P   POV B 601 "
        pdb=" O12 POV B 601 "
      ideal   model   delta    sigma   weight residual
      97.67  110.14  -12.47 3.00e+00 1.11e-01 1.73e+01
  angle pdb=" O13 POV B 601 "
        pdb=" P   POV B 601 "
        pdb=" O14 POV B 601 "
      ideal   model   delta    sigma   weight residual
     121.11  109.16   11.95 3.00e+00 1.11e-01 1.59e+01
  angle pdb=" C22 POV B 601 "
        pdb=" C21 POV B 601 "
        pdb=" O21 POV B 601 "
      ideal   model   delta    sigma   weight residual
     111.03  120.33   -9.30 3.00e+00 1.11e-01 9.61e+00
  angle pdb=" C32 POV B 601 "
        pdb=" C31 POV B 601 "
        pdb=" O31 POV B 601 "
      ideal   model   delta    sigma   weight residual
     110.66  119.95   -9.29 3.00e+00 1.11e-01 9.60e+00
  angle pdb=" N   POV B 601 "
        pdb=" C12 POV B 601 "
        pdb=" C11 POV B 601 "
      ideal   model   delta    sigma   weight residual
     118.03  108.89    9.14 3.00e+00 1.11e-01 9.28e+00
  ... (remaining 12090 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.27: 4952
       21.27 -    42.54: 362
       42.54 -    63.81: 63
       63.81 -    85.08: 27
       85.08 -   106.36: 18
  Dihedral angle restraints: 5422
    sinusoidal: 2338
      harmonic: 3084
  Sorted by residual:
  dihedral pdb=" CB  CYS A 324 "
           pdb=" SG  CYS A 324 "
           pdb=" SG  CYS A 339 "
           pdb=" CB  CYS A 339 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.31  -80.31     1      1.00e+01 1.00e-02 7.98e+01
  dihedral pdb=" CA  CYS A 331 "
           pdb=" C   CYS A 331 "
           pdb=" N   CYS A 332 "
           pdb=" CA  CYS A 332 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.60  -29.40     0      5.00e+00 4.00e-02 3.46e+01
  dihedral pdb=" CA  PHE A 328 "
           pdb=" C   PHE A 328 "
           pdb=" N   HIS A 329 "
           pdb=" CA  HIS A 329 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.02   22.98     0      5.00e+00 4.00e-02 2.11e+01
  ... (remaining 5419 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1089
       0.057 -    0.114: 190
       0.114 -    0.171: 18
       0.171 -    0.227: 2
       0.227 -    0.284: 1
  Chirality restraints: 1300
  Sorted by residual:
  chirality pdb=" C5  BMA D   3 "
            pdb=" C4  BMA D   3 "
            pdb=" C6  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.56    0.28 2.00e-01 2.50e+01 2.02e+00
  chirality pdb=" C2  MAN D   4 "
            pdb=" C1  MAN D   4 "
            pdb=" C3  MAN D   4 "
            pdb=" O2  MAN D   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.52    2.73   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 295 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.18   -0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 1297 not shown)

  Planarity restraints: 1526
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 177 "   -0.057 5.00e-02 4.00e+02   8.74e-02 1.22e+01
        pdb=" N   PRO C 178 "    0.151 5.00e-02 4.00e+02
        pdb=" CA  PRO C 178 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO C 178 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 281 "    0.058 5.00e-02 4.00e+02   8.58e-02 1.18e+01
        pdb=" N   PRO A 282 "   -0.148 5.00e-02 4.00e+02
        pdb=" CA  PRO A 282 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A 282 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 298 "    0.034 5.00e-02 4.00e+02   5.07e-02 4.11e+00
        pdb=" N   PRO A 299 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 299 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 299 "    0.028 5.00e-02 4.00e+02
  ... (remaining 1523 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1883
        2.78 -     3.31: 8331
        3.31 -     3.84: 14574
        3.84 -     4.37: 17165
        4.37 -     4.90: 29956
  Nonbonded interactions: 71909
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 173 "
            pdb=" OG1 THR A 178 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OE2 GLU B 285 "
            pdb=" NH2 ARG B 303 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" NE2 HIS A 329 "
            pdb=" OE2 GLU B 205 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" OH  TYR C 128 "
            pdb=" O3  GLC D   7 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" NH2 ARG A 342 "
            pdb=" OD2 ASP C 201 "
     model   vdw
     2.359 3.120
  ... (remaining 71904 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:             1.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.030
  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:             0.000
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
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   0.091   8959  Z= 0.292
  Angle     :  0.703  12.465  12095  Z= 0.353
  Chirality :  0.043   0.284   1300
  Planarity :  0.005   0.087   1525
  Dihedral  : 17.023 106.355   3395
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  8.93 %
    Favored  : 90.85 %
  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:  0.82 (0.26), residues: 1060
  helix:  2.15 (0.25), residues: 399
  sheet: -0.52 (0.37), residues: 206
  loop : -0.33 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 481 
 HIS   0.003   0.001   HIS C 170 
 PHE   0.015   0.001   PHE C 342 
 TYR   0.020   0.001   TYR C 338 
 ARG   0.006   0.000   ARG B 254 

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
REVERT: B  254 ARG cc_start: 0.8247 (mtp85) cc_final: 0.7965 (mtp85)
  outliers start: 2
  outliers final: 1
  residues processed: 100
  average time/residue: 0.2070
  time to fit residues: 30.1631
Evaluate side-chains
  94 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   66 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:   10.0000
   chunk 80 optimal weight:   10.0000
   chunk 44 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 54 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0570
   chunk 83 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 61 optimal weight:    0.4980
   chunk 96 optimal weight:    0.5980
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
A 325 ASN
B 459 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.194633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.124133 restraints weight = 9726.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 2.92
r_work: 0.3280 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.0760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8959  Z= 0.179
  Angle     :  0.553   9.527  12095  Z= 0.285
  Chirality :  0.042   0.232   1300
  Planarity :  0.005   0.064   1525
  Dihedral  : 12.152  89.178   1331
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  :  8.40 %
    Favored  : 89.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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:  1.11 (0.26), residues: 1060
  helix:  2.50 (0.25), residues: 386
  sheet: -0.18 (0.38), residues: 198
  loop : -0.30 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 481 
 HIS   0.004   0.001   HIS C 170 
 PHE   0.017   0.001   PHE C 113 
 TYR   0.016   0.001   TYR A 318 
 ARG   0.005   0.000   ARG B 254 

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.912 
Fit side-chains
REVERT: A  279 GLU cc_start: 0.7352 (mp0) cc_final: 0.7139 (mp0)
REVERT: C  168 PHE cc_start: 0.5314 (t80) cc_final: 0.4946 (t80)
REVERT: C  169 THR cc_start: 0.6923 (m) cc_final: 0.6544 (p)
REVERT: C  357 MET cc_start: 0.6315 (tpp) cc_final: 0.6040 (tpt)
  outliers start: 19
  outliers final: 10
  residues processed: 121
  average time/residue: 0.2044
  time to fit residues: 35.3876
Evaluate side-chains
  104 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  399 MET
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   78 SER
Chi-restraints excluded: chain C residue  195 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 90 optimal weight:    7.9990
   chunk 71 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 30 optimal weight:    0.2980
   chunk 46 optimal weight:    4.9990
   chunk 52 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 18 optimal weight:    0.4980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 459 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.195279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.124485 restraints weight = 9901.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 3.02
r_work: 0.3271 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.1038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8959  Z= 0.195
  Angle     :  0.531   6.947  12095  Z= 0.274
  Chirality :  0.042   0.220   1300
  Planarity :  0.004   0.054   1525
  Dihedral  : 10.491  87.776   1329
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  :  9.47 %
    Favored  : 88.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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:  1.20 (0.26), residues: 1060
  helix:  2.62 (0.25), residues: 388
  sheet: -0.22 (0.38), residues: 198
  loop : -0.27 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 481 
 HIS   0.003   0.001   HIS B 322 
 PHE   0.018   0.001   PHE C 113 
 TYR   0.014   0.001   TYR A 318 
 ARG   0.008   0.000   ARG B 254 

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.987 
Fit side-chains
REVERT: A  264 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7415 (ptm)
REVERT: A  279 GLU cc_start: 0.7358 (mp0) cc_final: 0.7125 (mp0)
REVERT: C  120 THR cc_start: 0.8301 (p) cc_final: 0.7970 (t)
REVERT: C  318 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7278 (pp)
REVERT: C  357 MET cc_start: 0.6299 (tpp) cc_final: 0.5967 (tpt)
  outliers start: 21
  outliers final: 13
  residues processed: 119
  average time/residue: 0.1877
  time to fit residues: 32.4643
Evaluate side-chains
  108 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain B residue    7 GLU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  459 HIS
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  201 ASP
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 54 optimal weight:    0.6980
   chunk 1 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   chunk 39 optimal weight:    0.1980
   chunk 59 optimal weight:    0.6980
   chunk 103 optimal weight:    7.9990
   chunk 73 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 100 optimal weight:    6.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
B 322 HIS
B 459 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.194489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.121820 restraints weight = 9862.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 2.48
r_work: 0.3286 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.1178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8959  Z= 0.225
  Angle     :  0.539   7.253  12095  Z= 0.276
  Chirality :  0.042   0.230   1300
  Planarity :  0.004   0.049   1525
  Dihedral  :  9.794  84.752   1329
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 10.44 %
    Favored  : 87.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.17 (0.26), residues: 1060
  helix:  2.67 (0.25), residues: 383
  sheet: -0.33 (0.38), residues: 196
  loop : -0.27 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 481 
 HIS   0.010   0.001   HIS B 459 
 PHE   0.017   0.001   PHE C 113 
 TYR   0.013   0.001   TYR A 318 
 ARG   0.006   0.000   ARG B 254 

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7334 (ptm)
REVERT: A  279 GLU cc_start: 0.7339 (mp0) cc_final: 0.7054 (mp0)
REVERT: B  405 ARG cc_start: 0.7629 (tpt170) cc_final: 0.7117 (ttp80)
REVERT: C  168 PHE cc_start: 0.5541 (t80) cc_final: 0.5210 (t80)
REVERT: C  318 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7192 (pp)
REVERT: C  357 MET cc_start: 0.6355 (tpp) cc_final: 0.6016 (tpt)
  outliers start: 19
  outliers final: 12
  residues processed: 115
  average time/residue: 0.1982
  time to fit residues: 32.4647
Evaluate side-chains
  112 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain B residue    7 GLU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  201 ASP
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 61 optimal weight:    0.0980
   chunk 2 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 81 optimal weight:    9.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
C  26 GLN
C  94 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.194401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.123799 restraints weight = 9794.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 2.94
r_work: 0.3282 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.1395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8959  Z= 0.182
  Angle     :  0.514   7.713  12095  Z= 0.264
  Chirality :  0.041   0.211   1300
  Planarity :  0.004   0.046   1525
  Dihedral  :  8.845  79.351   1329
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 10.76 %
    Favored  : 87.19 %
  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:  1.22 (0.26), residues: 1060
  helix:  2.76 (0.25), residues: 385
  sheet: -0.28 (0.38), residues: 190
  loop : -0.32 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 481 
 HIS   0.003   0.001   HIS C 170 
 PHE   0.016   0.001   PHE C 113 
 TYR   0.019   0.001   TYR C 150 
 ARG   0.009   0.000   ARG B 254 

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 1.007 
Fit side-chains
REVERT: A  279 GLU cc_start: 0.7498 (mp0) cc_final: 0.7189 (mp0)
REVERT: B  254 ARG cc_start: 0.8202 (mtp85) cc_final: 0.7888 (mtp85)
REVERT: B  285 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8539 (mp0)
REVERT: B  323 MET cc_start: 0.8420 (mmm) cc_final: 0.8113 (mmm)
REVERT: B  405 ARG cc_start: 0.7621 (tpt170) cc_final: 0.7167 (ttp-170)
REVERT: C   98 LYS cc_start: 0.7083 (ptmt) cc_final: 0.6818 (ptmt)
REVERT: C  120 THR cc_start: 0.8281 (p) cc_final: 0.7970 (t)
REVERT: C  318 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7244 (pp)
REVERT: C  357 MET cc_start: 0.6357 (tpp) cc_final: 0.6049 (tpp)
  outliers start: 19
  outliers final: 13
  residues processed: 119
  average time/residue: 0.1999
  time to fit residues: 33.8190
Evaluate side-chains
  116 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain B residue    7 GLU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  201 ASP
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 26 optimal weight:    8.9990
   chunk 83 optimal weight:    0.3980
   chunk 53 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
B 459 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.193514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.121547 restraints weight = 9736.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.40
r_work: 0.3305 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.1418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8959  Z= 0.217
  Angle     :  0.524   7.639  12095  Z= 0.269
  Chirality :  0.041   0.190   1300
  Planarity :  0.004   0.044   1525
  Dihedral  :  8.230  76.265   1329
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 11.52 %
    Favored  : 86.54 %
  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:  1.17 (0.26), residues: 1060
  helix:  2.71 (0.24), residues: 385
  sheet: -0.23 (0.38), residues: 188
  loop : -0.38 (0.29), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 481 
 HIS   0.003   0.001   HIS C 170 
 PHE   0.016   0.001   PHE C 113 
 TYR   0.013   0.001   TYR C 150 
 ARG   0.005   0.000   ARG B 254 

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
REVERT: A  279 GLU cc_start: 0.7518 (mp0) cc_final: 0.7226 (mp0)
REVERT: B  285 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8502 (mp0)
REVERT: B  287 PHE cc_start: 0.8069 (m-10) cc_final: 0.7862 (m-80)
REVERT: B  323 MET cc_start: 0.8431 (mmm) cc_final: 0.8109 (mmm)
REVERT: B  405 ARG cc_start: 0.7667 (tpt170) cc_final: 0.7228 (ttp-170)
REVERT: C  120 THR cc_start: 0.8299 (p) cc_final: 0.8007 (t)
REVERT: C  168 PHE cc_start: 0.5464 (t80) cc_final: 0.5221 (t80)
REVERT: C  318 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7269 (pp)
REVERT: C  357 MET cc_start: 0.6460 (tpp) cc_final: 0.6212 (tpp)
  outliers start: 18
  outliers final: 14
  residues processed: 113
  average time/residue: 0.2008
  time to fit residues: 32.3065
Evaluate side-chains
  113 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain B residue    7 GLU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  459 HIS
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  201 ASP
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 94 optimal weight:   10.0000
   chunk 30 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   chunk 95 optimal weight:    0.9990
   chunk 86 optimal weight:    6.9990
   chunk 89 optimal weight:    0.3980
   chunk 40 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
B 459 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.194182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.122271 restraints weight = 9855.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 2.41
r_work: 0.3315 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.1511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8959  Z= 0.182
  Angle     :  0.511   7.331  12095  Z= 0.263
  Chirality :  0.041   0.176   1300
  Planarity :  0.004   0.043   1525
  Dihedral  :  7.758  72.922   1329
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 11.63 %
    Favored  : 86.33 %
  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:  1.21 (0.26), residues: 1060
  helix:  2.78 (0.24), residues: 385
  sheet: -0.26 (0.38), residues: 188
  loop : -0.37 (0.29), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 481 
 HIS   0.006   0.001   HIS B 459 
 PHE   0.015   0.001   PHE C 113 
 TYR   0.012   0.001   TYR C 150 
 ARG   0.008   0.000   ARG B 254 

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 1.032 
Fit side-chains
   revert: symmetry clash
REVERT: B  254 ARG cc_start: 0.8184 (mtp85) cc_final: 0.7803 (mtp85)
REVERT: B  258 MET cc_start: 0.8077 (mtp) cc_final: 0.7435 (mtp)
REVERT: B  285 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8515 (mp0)
REVERT: B  323 MET cc_start: 0.8432 (mmm) cc_final: 0.8108 (mmm)
REVERT: B  405 ARG cc_start: 0.7675 (tpt170) cc_final: 0.7247 (ttp80)
REVERT: C  120 THR cc_start: 0.8328 (p) cc_final: 0.8054 (t)
REVERT: C  318 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7249 (pp)
REVERT: C  357 MET cc_start: 0.6312 (tpp) cc_final: 0.6082 (tpp)
  outliers start: 19
  outliers final: 13
  residues processed: 112
  average time/residue: 0.1969
  time to fit residues: 31.8589
Evaluate side-chains
  110 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain B residue    7 GLU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  201 ASP
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 50 optimal weight:    4.9990
   chunk 92 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0000
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
B 459 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.194035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.123433 restraints weight = 9975.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 2.83
r_work: 0.3297 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.1577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8959  Z= 0.189
  Angle     :  0.509   6.902  12095  Z= 0.262
  Chirality :  0.041   0.165   1300
  Planarity :  0.004   0.042   1525
  Dihedral  :  7.293  69.841   1329
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 12.06 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.19 (0.26), residues: 1060
  helix:  2.76 (0.24), residues: 385
  sheet: -0.27 (0.38), residues: 188
  loop : -0.37 (0.29), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 481 
 HIS   0.003   0.001   HIS C 170 
 PHE   0.015   0.001   PHE C 113 
 TYR   0.011   0.001   TYR C 150 
 ARG   0.006   0.000   ARG B 254 

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 1.012 
Fit side-chains
REVERT: B  254 ARG cc_start: 0.8174 (mtp85) cc_final: 0.7784 (mtp85)
REVERT: B  258 MET cc_start: 0.8099 (mtp) cc_final: 0.7488 (mtp)
REVERT: B  285 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8519 (mp0)
REVERT: B  323 MET cc_start: 0.8414 (mmm) cc_final: 0.8088 (mmm)
REVERT: B  405 ARG cc_start: 0.7685 (tpt170) cc_final: 0.7224 (ttp80)
REVERT: C   98 LYS cc_start: 0.7138 (ptmt) cc_final: 0.6895 (ptmt)
REVERT: C  120 THR cc_start: 0.8331 (p) cc_final: 0.8066 (t)
REVERT: C  318 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7248 (pp)
REVERT: C  357 MET cc_start: 0.6311 (tpp) cc_final: 0.6082 (tpp)
  outliers start: 17
  outliers final: 14
  residues processed: 113
  average time/residue: 0.1941
  time to fit residues: 31.9079
Evaluate side-chains
  113 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain B residue    7 GLU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   56 PHE
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  201 ASP
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 55 optimal weight:    0.0970
   chunk 47 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 94 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 63 optimal weight:    0.9990
   chunk 90 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   chunk 50 optimal weight:    3.9990
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.193790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.121714 restraints weight = 9899.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 2.42
r_work: 0.3311 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3156 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8959  Z= 0.207
  Angle     :  0.513   6.924  12095  Z= 0.263
  Chirality :  0.041   0.153   1300
  Planarity :  0.004   0.042   1525
  Dihedral  :  6.963  68.675   1329
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 12.59 %
    Favored  : 85.68 %
  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:  1.16 (0.26), residues: 1060
  helix:  2.72 (0.24), residues: 385
  sheet: -0.29 (0.38), residues: 188
  loop : -0.39 (0.29), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 481 
 HIS   0.003   0.001   HIS C 170 
 PHE   0.016   0.001   PHE C 113 
 TYR   0.011   0.001   TYR C 150 
 ARG   0.005   0.000   ARG B 254 

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.950 
Fit side-chains
REVERT: B  254 ARG cc_start: 0.8180 (mtp85) cc_final: 0.7796 (mtp85)
REVERT: B  258 MET cc_start: 0.8085 (mtp) cc_final: 0.7511 (mtp)
REVERT: B  285 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8529 (mp0)
REVERT: B  323 MET cc_start: 0.8417 (mmm) cc_final: 0.8111 (mmm)
REVERT: B  405 ARG cc_start: 0.7672 (tpt170) cc_final: 0.7253 (ttp80)
REVERT: C   98 LYS cc_start: 0.7164 (ptmt) cc_final: 0.6911 (ptmt)
REVERT: C  120 THR cc_start: 0.8357 (p) cc_final: 0.8116 (t)
REVERT: C  318 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7289 (pp)
REVERT: C  357 MET cc_start: 0.6383 (tpp) cc_final: 0.6136 (tpp)
  outliers start: 16
  outliers final: 14
  residues processed: 113
  average time/residue: 0.1900
  time to fit residues: 31.3177
Evaluate side-chains
  111 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain B residue    7 GLU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  201 ASP
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0870
   chunk 92 optimal weight:    5.9990
   chunk 88 optimal weight:    5.9990
   chunk 5 optimal weight:    0.3980
   chunk 15 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 104 optimal weight:    7.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.8760

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.193612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.121397 restraints weight = 9894.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.42
r_work: 0.3302 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3147 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8959  Z= 0.216
  Angle     :  0.517   6.848  12095  Z= 0.267
  Chirality :  0.041   0.147   1300
  Planarity :  0.004   0.042   1525
  Dihedral  :  6.826  69.096   1329
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 12.59 %
    Favored  : 85.47 %
  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:  1.17 (0.26), residues: 1060
  helix:  2.72 (0.24), residues: 385
  sheet: -0.30 (0.38), residues: 190
  loop : -0.35 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 481 
 HIS   0.003   0.001   HIS C 170 
 PHE   0.016   0.001   PHE C 113 
 TYR   0.010   0.001   TYR C 150 
 ARG   0.006   0.000   ARG B 254 

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.991 
Fit side-chains
REVERT: B  254 ARG cc_start: 0.8189 (mtp85) cc_final: 0.7803 (mtp85)
REVERT: B  258 MET cc_start: 0.8111 (mtp) cc_final: 0.7530 (mtp)
REVERT: B  285 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8522 (mp0)
REVERT: B  323 MET cc_start: 0.8419 (mmm) cc_final: 0.8111 (mmm)
REVERT: B  405 ARG cc_start: 0.7683 (tpt170) cc_final: 0.7249 (ttp80)
REVERT: C   21 VAL cc_start: 0.7681 (t) cc_final: 0.7304 (p)
REVERT: C   98 LYS cc_start: 0.7149 (ptmt) cc_final: 0.6885 (ptmt)
REVERT: C  120 THR cc_start: 0.8352 (p) cc_final: 0.8095 (t)
REVERT: C  318 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7253 (pp)
REVERT: C  357 MET cc_start: 0.6352 (tpp) cc_final: 0.6111 (tpp)
  outliers start: 18
  outliers final: 15
  residues processed: 113
  average time/residue: 0.1945
  time to fit residues: 31.6126
Evaluate side-chains
  114 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain B residue    7 GLU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  248 ILE
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   56 PHE
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  201 ASP
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 81 optimal weight:    8.9990
   chunk 72 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 97 optimal weight:    0.2980
   chunk 24 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   chunk 74 optimal weight:    0.8980
   chunk 61 optimal weight:    0.5980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.194395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.122628 restraints weight = 9895.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 2.42
r_work: 0.3316 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8959  Z= 0.184
  Angle     :  0.502   6.863  12095  Z= 0.261
  Chirality :  0.040   0.171   1300
  Planarity :  0.004   0.042   1525
  Dihedral  :  6.556  67.753   1329
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 12.59 %
    Favored  : 85.58 %
  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:  1.20 (0.26), residues: 1060
  helix:  2.81 (0.24), residues: 385
  sheet: -0.26 (0.39), residues: 188
  loop : -0.40 (0.29), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 481 
 HIS   0.003   0.001   HIS C 170 
 PHE   0.015   0.001   PHE C 113 
 TYR   0.011   0.001   TYR C 150 
 ARG   0.005   0.000   ARG B 254 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5872.35 seconds
wall clock time: 104 minutes 31.51 seconds (6271.51 seconds total)