Starting phenix.real_space_refine
on Tue Mar  3 17:12:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7d76_30602/03_2026/7d76_30602.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7d76_30602/03_2026/7d76_30602.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7d76_30602/03_2026/7d76_30602.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7d76_30602/03_2026/7d76_30602.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7d76_30602/03_2026/7d76_30602.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7d76_30602/03_2026/7d76_30602.map"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     Cl      1      4.86       5
     C    4521      2.51       5
     N    1174      2.21       5
     O    1273      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7015
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1707
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 210}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "R"
      Number of atoms: 2107
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 265, 2097
          Classifications: {'peptide': 265}
          Link IDs: {'PTRANS': 4, 'TRANS': 260}
      Conformer: "B"
        Number of residues, atoms: 265, 2097
          Classifications: {'peptide': 265}
          Link IDs: {'PTRANS': 4, 'TRANS': 260}
          bond proxies already assigned to first conformer: 2143
    Chain: "A"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'PLM': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'PLM:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "R"
      Number of atoms: 155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 155
          Unusual residues: {'CLR': 2, 'GXR': 1, 'PLM': 2, 'Y01': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AHIS R 309 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS R 309 " occ=0.50
  Time building chain proxies: 2.05, per 1000 atoms: 0.29
  Number of scatterers: 7015
  At special positions: 0
  Unit cell: (79.092, 111.54, 111.54, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      46     16.00
     O    1273      8.00
     N    1174      7.00
     C    4521      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 338 " - pdb=" SG  CYS R 420 " distance=2.04

  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
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.75
  Conformation dependent library (CDL) restraints added in 271.3 milliseconds
  

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1628

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 9 sheets defined
      43.2% alpha, 15.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.601A  pdb=" N   ALA A  31 " --> pdb=" O   GLY A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 49
      removed outlier: 3.944A  pdb=" N   ILE A  49 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 3.720A  pdb=" N   TRP A 212 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 217
      removed outlier: 3.674A  pdb=" N   GLU A 217 " --> pdb=" O   HIS A 214 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 214 through 217'
    Processing helix  chain 'A' and resid 242 through 256
      removed outlier: 4.491A  pdb=" N   GLU A 246 " --> pdb=" O   ASN A 242 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ASN A 256 " --> pdb=" O   ASP A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 282
      removed outlier: 4.262A  pdb=" N   LYS A 280 " --> pdb=" O   GLY A 276 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   LYS A 281 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 310
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.839A  pdb=" N   ILE A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.601A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.500A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.719A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'R' and resid 264 through 297
    Processing helix  chain 'R' and resid 304 through 329
    Processing helix  chain 'R' and resid 334 through 368
      removed outlier: 3.611A  pdb=" N   CYS R 338 " --> pdb=" O   SER R 334 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA R 340 " --> pdb=" O   ALA R 336 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 377 through 400
      Proline residue:  R 390  - end of helix
      removed outlier: 3.675A  pdb=" N   ALA R 400 " --> pdb=" O   GLY R 396 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 428 through 435
    Processing helix  chain 'R' and resid 435 through 464
      removed outlier: 4.339A  pdb=" N   ARG R 462 " --> pdb=" O   PHE R 458 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ALA R 463 " --> pdb=" O   THR R 459 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 471 through 496
      removed outlier: 4.167A  pdb=" N   LEU R 477 " --> pdb=" O   ARG R 473 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU R 485 " --> pdb=" O   GLY R 481 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   TRP R 490 " --> pdb=" O   VAL R 486 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 502 through 525
      removed outlier: 3.619A  pdb=" N   PHE R 506 " --> pdb=" O   THR R 502 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ILE R 517 " --> pdb=" O   GLN R 513 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 188
      removed outlier: 6.371A  pdb=" N   VAL A  34 " --> pdb=" O   ARG A 198 " (cutoff:3.500A)
      removed outlier: 7.606A  pdb=" N   PHE A 200 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ALA A 221 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.559A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.740A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.126A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.049A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151
      removed outlier: 4.032A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.849A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.693A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.656A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278
      removed outlier: 6.612A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 406 through 408
      removed outlier: 3.662A  pdb=" N   LEU R 417 " --> pdb=" O   ILE R 408 " (cutoff:3.500A)

    340 hydrogen bonds defined for protein.
    1000 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.07

  Time building geometry restraints manager: 0.87 seconds

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

  Histogram of bond lengths:
        1.19 -     1.33: 1249
        1.33 -     1.46: 2695
        1.46 -     1.60: 3152
        1.60 -     1.73: 5
        1.73 -     1.87: 65
  Bond restraints: 7166
  Sorted by residual:
  bond pdb=" CAS Y01 R 601 "
       pdb=" CAU Y01 R 601 "
    ideal  model  delta    sigma   weight residual
    1.530  1.304  0.226 2.00e-02 2.50e+03 1.28e+02
  bond pdb=" CBE Y01 R 601 "
       pdb=" CBI Y01 R 601 "
    ideal  model  delta    sigma   weight residual
    1.550  1.374  0.176 2.00e-02 2.50e+03 7.73e+01
  bond pdb=" C   ASN A 347 "
       pdb=" N   LEU A 348 "
    ideal  model  delta    sigma   weight residual
    1.335  1.453 -0.118 1.35e-02 5.49e+03 7.63e+01
  bond pdb=" CAS Y01 R 601 "
       pdb=" CBF Y01 R 601 "
    ideal  model  delta    sigma   weight residual
    1.533  1.365  0.168 2.00e-02 2.50e+03 7.07e+01
  bond pdb=" CBF Y01 R 601 "
       pdb=" CBH Y01 R 601 "
    ideal  model  delta    sigma   weight residual
    1.550  1.691 -0.141 2.00e-02 2.50e+03 4.96e+01
  ... (remaining 7161 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.87: 9414
        1.87 -     3.74: 239
        3.74 -     5.61: 40
        5.61 -     7.48: 11
        7.48 -     9.35: 9
  Bond angle restraints: 9713
  Sorted by residual:
  angle pdb=" C   ALA R 337 "
        pdb=" N   CYS R 338 "
        pdb=" CA  CYS R 338 "
      ideal   model   delta    sigma   weight residual
     121.94  112.94    9.00 2.00e+00 2.50e-01 2.02e+01
  angle pdb=" CA  CYS R 420 "
        pdb=" CB  CYS R 420 "
        pdb=" SG  CYS R 420 "
      ideal   model   delta    sigma   weight residual
     114.40  122.00   -7.60 2.30e+00 1.89e-01 1.09e+01
  angle pdb=" C   CYS R 420 "
        pdb=" N   TRP R 421 "
        pdb=" CA  TRP R 421 "
      ideal   model   delta    sigma   weight residual
     121.74  126.82   -5.08 1.58e+00 4.01e-01 1.04e+01
  angle pdb=" CBD Y01 R 601 "
        pdb=" CBG Y01 R 601 "
        pdb=" CBI Y01 R 601 "
      ideal   model   delta    sigma   weight residual
     115.11  105.76    9.35 3.00e+00 1.11e-01 9.71e+00
  angle pdb=" CBB Y01 R 601 "
        pdb=" CBE Y01 R 601 "
        pdb=" CBI Y01 R 601 "
      ideal   model   delta    sigma   weight residual
     119.27  110.22    9.05 3.00e+00 1.11e-01 9.09e+00
  ... (remaining 9708 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.02: 4065
       20.02 -    40.04: 311
       40.04 -    60.05: 49
       60.05 -    80.07: 7
       80.07 -   100.09: 5
  Dihedral angle restraints: 4437
    sinusoidal: 1911
      harmonic: 2526
  Sorted by residual:
  dihedral pdb=" CB  CYS R 338 "
           pdb=" SG  CYS R 338 "
           pdb=" SG  CYS R 420 "
           pdb=" CB  CYS R 420 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  165.80  -72.80     1      1.00e+01 1.00e-02 6.76e+01
  dihedral pdb=" CA  CYS R 338 "
           pdb=" C   CYS R 338 "
           pdb=" N   TRP R 339 "
           pdb=" CA  TRP R 339 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.32   24.68     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" O1  GXR R 604 "
           pdb=" C15 GXR R 604 "
           pdb=" C5  GXR R 604 "
           pdb=" O3  GXR R 604 "
      ideal   model   delta sinusoidal    sigma   weight residual
     167.26   67.17  100.09     1      3.00e+01 1.11e-03 1.25e+01
  ... (remaining 4434 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.107: 1065
       0.107 -    0.215: 35
       0.215 -    0.322: 7
       0.322 -    0.429: 2
       0.429 -    0.537: 1
  Chirality restraints: 1110
  Sorted by residual:
  chirality pdb=" CBG Y01 R 601 "
            pdb=" CAQ Y01 R 601 "
            pdb=" CBD Y01 R 601 "
            pdb=" CBI Y01 R 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.87    0.54 2.00e-01 2.50e+01 7.20e+00
  chirality pdb=" C14 CLR R 605 "
            pdb=" C13 CLR R 605 "
            pdb=" C15 CLR R 605 "
            pdb=" C8  CLR R 605 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.70    0.39 2.00e-01 2.50e+01 3.75e+00
  chirality pdb=" C14 CLR R 606 "
            pdb=" C13 CLR R 606 "
            pdb=" C15 CLR R 606 "
            pdb=" C8  CLR R 606 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.70    0.38 2.00e-01 2.50e+01 3.60e+00
  ... (remaining 1107 not shown)

  Planarity restraints: 1201
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 GXR R 604 "   -0.008 2.00e-02 2.50e+03   1.64e-01 3.35e+02
        pdb=" C13 GXR R 604 "   -0.183 2.00e-02 2.50e+03
        pdb=" C14 GXR R 604 "    0.194 2.00e-02 2.50e+03
        pdb=" C19 GXR R 604 "    0.175 2.00e-02 2.50e+03
        pdb=" C22 GXR R 604 "   -0.179 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 347 "    0.017 2.00e-02 2.50e+03   3.22e-02 1.04e+01
        pdb=" C   ASN A 347 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   ASN A 347 "    0.021 2.00e-02 2.50e+03
        pdb=" N   LEU A 348 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 105 "    0.014 2.00e-02 2.50e+03   1.42e-02 4.05e+00
        pdb=" CG  TYR B 105 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 105 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 105 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 105 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 105 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 105 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 105 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1198 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 298
        2.71 -     3.26: 7066
        3.26 -     3.81: 10800
        3.81 -     4.35: 13812
        4.35 -     4.90: 23764
  Nonbonded interactions: 55740
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.167 3.040
  nonbonded pdb=" O   LYS B  57 "
            pdb=" OG  SER B  74 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" O   ALA R 430 "
            pdb=" OG1 THR R 434 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OD1 ASP A 341 "
            pdb=" ND2 ASN R 472 "
     model   vdw
     2.226 3.120
  nonbonded pdb=" OE2 GLU A 187 "
            pdb=" NH1 ARG A 198 "
     model   vdw
     2.256 3.120
  ... (remaining 55735 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=0.50 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:             0.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.800
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
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      :  0.008   0.226   7168  Z= 0.382
  Angle     :  0.790   9.350   9715  Z= 0.405
  Chirality :  0.054   0.537   1110
  Planarity :  0.006   0.164   1201
  Dihedral  : 14.402 100.088   2806
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.55 (0.26), residues: 867
  helix:  0.07 (0.26), residues: 351
  sheet: -3.13 (0.32), residues: 183
  loop : -2.68 (0.28), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B   8 
 TYR   0.035   0.002   TYR B 105 
 PHE   0.018   0.001   PHE R 345 
 TRP   0.016   0.002   TRP B 332 
 HIS   0.004   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00760 ( 7166)
  covalent geometry    : angle       0.78705 ( 9713)
  SS BOND              : bond        0.00633 (    1)
  SS BOND              : angle       4.74519 (    2)
  hydrogen bonds       : bond        0.14202 (  340)
  hydrogen bonds       : angle       5.79891 ( 1000)
  Misc. bond           : bond        0.07001 (    1)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 MET cc_start: 0.8608 (tpp) cc_final: 0.8118 (tpp)
REVERT: G   36 ASP cc_start: 0.8444 (m-30) cc_final: 0.8128 (m-30)
REVERT: R  280 MET cc_start: 0.7017 (mtm) cc_final: 0.6708 (mtp)
REVERT: R  299 ARG cc_start: 0.7108 (ttp-170) cc_final: 0.6620 (tmm-80)
REVERT: R  401 ASN cc_start: 0.7979 (m-40) cc_final: 0.7741 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1066
  time to fit residues: 17.7523
Evaluate side-chains
  100 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    4.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 194 ASN
A 214 HIS
A 295 ASN
** B  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 HIS
R 266 HIS
R 346 HIS
R 362 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.160864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.120658 restraints weight = 8398.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.61
r_work: 0.3286 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3289
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3289
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7168  Z= 0.151
  Angle     :  0.603  12.292   9715  Z= 0.305
  Chirality :  0.043   0.204   1110
  Planarity :  0.004   0.041   1201
  Dihedral  :  8.101  57.990   1269
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 10.75 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.28), residues: 867
  helix:  1.59 (0.27), residues: 352
  sheet: -2.44 (0.36), residues: 172
  loop : -2.22 (0.30), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG R 411 
 TYR   0.019   0.001   TYR B 105 
 PHE   0.017   0.001   PHE R 292 
 TRP   0.011   0.002   TRP B 297 
 HIS   0.004   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 7166)
  covalent geometry    : angle       0.60160 ( 9713)
  SS BOND              : bond        0.00527 (    1)
  SS BOND              : angle       3.37284 (    2)
  hydrogen bonds       : bond        0.04254 (  340)
  hydrogen bonds       : angle       4.11920 ( 1000)
  Misc. bond           : bond        0.00001 (    1)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ASP cc_start: 0.8024 (t0) cc_final: 0.7788 (t0)
REVERT: A  244 MET cc_start: 0.8687 (tpp) cc_final: 0.8128 (tpp)
REVERT: A  277 GLU cc_start: 0.8646 (tp30) cc_final: 0.8369 (tp30)
REVERT: A  316 ASN cc_start: 0.8109 (t0) cc_final: 0.7865 (t0)
REVERT: B  170 ASP cc_start: 0.8469 (t70) cc_final: 0.8222 (t0)
REVERT: B  184 THR cc_start: 0.8928 (m) cc_final: 0.8683 (p)
REVERT: B  219 ARG cc_start: 0.8042 (mtt-85) cc_final: 0.7466 (mtt-85)
REVERT: B  241 PHE cc_start: 0.9155 (p90) cc_final: 0.8858 (p90)
REVERT: G   48 ASP cc_start: 0.8015 (t0) cc_final: 0.7650 (t70)
  outliers start: 10
  outliers final: 5
  residues processed: 121
  average time/residue: 0.0837
  time to fit residues: 13.5057
Evaluate side-chains
  111 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 106
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain R residue  324 LEU
Chi-restraints excluded: chain R residue  503 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0000
   chunk 80 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   overall best weight:    1.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 312 ASN
B  16 ASN
B  54 HIS
R 266 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.165829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.122390 restraints weight = 21004.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 4.21
r_work: 0.3219 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3221
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3221
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.1553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7168  Z= 0.136
  Angle     :  0.568  12.499   9715  Z= 0.286
  Chirality :  0.042   0.174   1110
  Planarity :  0.003   0.038   1201
  Dihedral  :  6.755  54.888   1269
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 12.93 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.29), residues: 867
  helix:  2.13 (0.28), residues: 355
  sheet: -2.09 (0.38), residues: 169
  loop : -2.00 (0.31), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 411 
 TYR   0.013   0.001   TYR B 105 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.011   0.001   TRP R 339 
 HIS   0.002   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 7166)
  covalent geometry    : angle       0.56601 ( 9713)
  SS BOND              : bond        0.00598 (    1)
  SS BOND              : angle       3.40879 (    2)
  hydrogen bonds       : bond        0.03961 (  340)
  hydrogen bonds       : angle       3.85994 ( 1000)
  Misc. bond           : bond        0.00004 (    1)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A   42 ASP cc_start: 0.8113 (t0) cc_final: 0.7860 (t0)
REVERT: A  244 MET cc_start: 0.8723 (tpp) cc_final: 0.8129 (tpp)
REVERT: A  277 GLU cc_start: 0.8843 (tp30) cc_final: 0.8521 (tp30)
REVERT: B  170 ASP cc_start: 0.8516 (t70) cc_final: 0.8236 (t0)
REVERT: B  184 THR cc_start: 0.8974 (m) cc_final: 0.8732 (p)
REVERT: B  219 ARG cc_start: 0.8082 (mtt-85) cc_final: 0.7558 (mtt-85)
REVERT: B  228 ASP cc_start: 0.8737 (m-30) cc_final: 0.8412 (m-30)
REVERT: B  234 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8326 (m-80)
REVERT: B  241 PHE cc_start: 0.9157 (p90) cc_final: 0.8902 (p90)
REVERT: G   48 ASP cc_start: 0.8051 (t0) cc_final: 0.7655 (t70)
REVERT: R  326 ASN cc_start: 0.8716 (m-40) cc_final: 0.8472 (m-40)
REVERT: R  414 ARG cc_start: 0.5564 (tpt170) cc_final: 0.4889 (mmm-85)
  outliers start: 14
  outliers final: 8
  residues processed: 126
  average time/residue: 0.0794
  time to fit residues: 13.5940
Evaluate side-chains
  119 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain R residue  324 LEU
Chi-restraints excluded: chain R residue  366 LEU
Chi-restraints excluded: chain R residue  418 GLU
Chi-restraints excluded: chain R residue  503 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 79 optimal weight:    0.0970
   chunk 34 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0570
   chunk 48 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.6096

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

Flipped N/Q/H residues before XYZ refinement:
R 266 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.168634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.128857 restraints weight = 13500.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 3.52
r_work: 0.3331 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3316
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3316 r_free = 0.3316    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3316 r_free = 0.3316    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3316
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.1931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7168  Z= 0.104
  Angle     :  0.533  12.499   9715  Z= 0.270
  Chirality :  0.041   0.149   1110
  Planarity :  0.003   0.037   1201
  Dihedral  :  6.028  55.891   1269
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 14.01 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.30), residues: 867
  helix:  2.49 (0.28), residues: 359
  sheet: -1.82 (0.38), residues: 174
  loop : -1.76 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  19 
 TYR   0.008   0.001   TYR B 105 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.011   0.001   TRP R 339 
 HIS   0.002   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 7166)
  covalent geometry    : angle       0.53254 ( 9713)
  SS BOND              : bond        0.00828 (    1)
  SS BOND              : angle       2.25812 (    2)
  hydrogen bonds       : bond        0.03401 (  340)
  hydrogen bonds       : angle       3.57693 ( 1000)
  Misc. bond           : bond        0.00014 (    1)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A  244 MET cc_start: 0.8683 (tpp) cc_final: 0.8089 (tpp)
REVERT: A  246 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7395 (mp0)
REVERT: A  280 LYS cc_start: 0.8582 (mtmm) cc_final: 0.8308 (ptpp)
REVERT: B  170 ASP cc_start: 0.8501 (t70) cc_final: 0.8188 (t0)
REVERT: B  184 THR cc_start: 0.8950 (m) cc_final: 0.8698 (p)
REVERT: B  219 ARG cc_start: 0.8086 (mtt-85) cc_final: 0.7730 (mtt-85)
REVERT: B  228 ASP cc_start: 0.8648 (m-30) cc_final: 0.8191 (m-30)
REVERT: B  234 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8249 (m-80)
REVERT: B  241 PHE cc_start: 0.9092 (p90) cc_final: 0.8846 (p90)
REVERT: G   48 ASP cc_start: 0.8160 (t0) cc_final: 0.7733 (t70)
REVERT: R  326 ASN cc_start: 0.8560 (m-40) cc_final: 0.8321 (m-40)
REVERT: R  414 ARG cc_start: 0.5625 (tpt170) cc_final: 0.4916 (mmm-85)
  outliers start: 14
  outliers final: 6
  residues processed: 135
  average time/residue: 0.0771
  time to fit residues: 14.2584
Evaluate side-chains
  122 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 115
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain R residue  324 LEU
Chi-restraints excluded: chain R residue  485 LEU
Chi-restraints excluded: chain R residue  503 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   chunk 51 optimal weight:    8.9990
   chunk 45 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 80 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
R 266 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.163755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.124473 restraints weight = 22043.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 6.06
r_work: 0.3139 rms_B_bonded: 5.42 restraints_weight: 2.0000
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3140
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3140
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   7168  Z= 0.189
  Angle     :  0.604  12.208   9715  Z= 0.310
  Chirality :  0.044   0.165   1110
  Planarity :  0.003   0.038   1201
  Dihedral  :  6.479  51.657   1269
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.10 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.30), residues: 867
  helix:  2.43 (0.27), residues: 356
  sheet: -1.77 (0.39), residues: 174
  loop : -1.75 (0.32), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 411 
 TYR   0.010   0.001   TYR B  59 
 PHE   0.017   0.002   PHE R 345 
 TRP   0.012   0.002   TRP R 355 
 HIS   0.002   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 7166)
  covalent geometry    : angle       0.60074 ( 9713)
  SS BOND              : bond        0.01046 (    1)
  SS BOND              : angle       4.29443 (    2)
  hydrogen bonds       : bond        0.04201 (  340)
  hydrogen bonds       : angle       3.85697 ( 1000)
  Misc. bond           : bond        0.00030 (    1)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A  244 MET cc_start: 0.8723 (tpp) cc_final: 0.8039 (tpp)
REVERT: A  281 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8730 (mmmt)
REVERT: A  316 ASN cc_start: 0.8134 (t0) cc_final: 0.7897 (t0)
REVERT: B  170 ASP cc_start: 0.8507 (t70) cc_final: 0.8147 (t0)
REVERT: B  219 ARG cc_start: 0.8163 (mtt-85) cc_final: 0.7631 (mtt-85)
REVERT: B  228 ASP cc_start: 0.8772 (m-30) cc_final: 0.8495 (m-30)
REVERT: B  234 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8328 (m-80)
REVERT: R  414 ARG cc_start: 0.5720 (tpt170) cc_final: 0.5005 (mmm-85)
  outliers start: 17
  outliers final: 12
  residues processed: 120
  average time/residue: 0.0724
  time to fit residues: 11.9818
Evaluate side-chains
  118 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue  324 LEU
Chi-restraints excluded: chain R residue  366 LEU
Chi-restraints excluded: chain R residue  418 GLU
Chi-restraints excluded: chain R residue  485 LEU
Chi-restraints excluded: chain R residue  503 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 75 optimal weight:    0.6980
   chunk 11 optimal weight:    0.3980
   chunk 7 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 194 ASN
B 110 ASN
R 266 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.163259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.125915 restraints weight = 17433.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 4.51
r_work: 0.3227 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3229
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3229
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7168  Z= 0.109
  Angle     :  0.539  12.471   9715  Z= 0.272
  Chirality :  0.041   0.146   1110
  Planarity :  0.003   0.038   1201
  Dihedral  :  5.973  54.497   1269
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.10 %
    Favored  : 82.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.30), residues: 867
  helix:  2.62 (0.28), residues: 359
  sheet: -1.69 (0.38), residues: 174
  loop : -1.61 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 349 
 TYR   0.008   0.001   TYR B  59 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.011   0.001   TRP R 339 
 HIS   0.006   0.001   HIS R 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 7166)
  covalent geometry    : angle       0.53807 ( 9713)
  SS BOND              : bond        0.00830 (    1)
  SS BOND              : angle       2.74805 (    2)
  hydrogen bonds       : bond        0.03482 (  340)
  hydrogen bonds       : angle       3.57989 ( 1000)
  Misc. bond           : bond        0.00005 (    1)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.8308 (m-40) cc_final: 0.7541 (t0)
REVERT: A  244 MET cc_start: 0.8722 (tpp) cc_final: 0.8050 (tpp)
REVERT: A  316 ASN cc_start: 0.8124 (t0) cc_final: 0.7892 (t0)
REVERT: B  170 ASP cc_start: 0.8489 (t70) cc_final: 0.8125 (t0)
REVERT: B  219 ARG cc_start: 0.8085 (mtt-85) cc_final: 0.7751 (mtt-85)
REVERT: B  228 ASP cc_start: 0.8623 (m-30) cc_final: 0.7985 (m-30)
REVERT: B  234 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.8280 (m-80)
REVERT: B  292 PHE cc_start: 0.8485 (m-80) cc_final: 0.8261 (m-10)
REVERT: G   48 ASP cc_start: 0.8179 (t0) cc_final: 0.7729 (t70)
REVERT: R  326 ASN cc_start: 0.8577 (m-40) cc_final: 0.8324 (m-40)
REVERT: R  414 ARG cc_start: 0.5611 (tpt170) cc_final: 0.4883 (mmm-85)
  outliers start: 20
  outliers final: 13
  residues processed: 127
  average time/residue: 0.0779
  time to fit residues: 13.5448
Evaluate side-chains
  122 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain R residue  266 HIS
Chi-restraints excluded: chain R residue  324 LEU
Chi-restraints excluded: chain R residue  366 LEU
Chi-restraints excluded: chain R residue  485 LEU
Chi-restraints excluded: chain R residue  503 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 33 optimal weight:    0.3980
   chunk 26 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0030
   chunk 44 optimal weight:    0.0870
   chunk 7 optimal weight:    0.0370
   chunk 10 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.3046

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

Flipped N/Q/H residues before XYZ refinement:
R 266 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.171703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.133410 restraints weight = 20731.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 5.83
r_work: 0.3235 rms_B_bonded: 5.40 restraints_weight: 2.0000
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3233
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3233
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.2317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7168  Z= 0.098
  Angle     :  0.546  12.683   9715  Z= 0.274
  Chirality :  0.040   0.149   1110
  Planarity :  0.003   0.038   1201
  Dihedral  :  5.725  53.706   1269
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 16.60 %
    Favored  : 81.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.30), residues: 867
  helix:  2.77 (0.28), residues: 359
  sheet: -1.51 (0.39), residues: 174
  loop : -1.51 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  19 
 TYR   0.008   0.001   TYR R 290 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.011   0.001   TRP B 297 
 HIS   0.025   0.001   HIS R 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 7166)
  covalent geometry    : angle       0.54218 ( 9713)
  SS BOND              : bond        0.00499 (    1)
  SS BOND              : angle       4.40501 (    2)
  hydrogen bonds       : bond        0.03239 (  340)
  hydrogen bonds       : angle       3.47306 ( 1000)
  Misc. bond           : bond        0.00011 (    1)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.8117 (m-40) cc_final: 0.7501 (t0)
REVERT: A  244 MET cc_start: 0.8725 (tpp) cc_final: 0.8085 (tpp)
REVERT: A  246 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7334 (mp0)
REVERT: B  170 ASP cc_start: 0.8514 (t70) cc_final: 0.8148 (t0)
REVERT: B  200 VAL cc_start: 0.8869 (m) cc_final: 0.8636 (p)
REVERT: B  219 ARG cc_start: 0.8148 (mtt-85) cc_final: 0.7835 (mtt-85)
REVERT: B  228 ASP cc_start: 0.8747 (m-30) cc_final: 0.8141 (m-30)
REVERT: B  234 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8359 (m-80)
REVERT: B  256 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.8303 (mtp180)
REVERT: G   48 ASP cc_start: 0.8212 (t0) cc_final: 0.7875 (t0)
REVERT: R  326 ASN cc_start: 0.8527 (m-40) cc_final: 0.8301 (m-40)
REVERT: R  414 ARG cc_start: 0.5604 (tpt170) cc_final: 0.4854 (mmm-85)
  outliers start: 15
  outliers final: 10
  residues processed: 126
  average time/residue: 0.0787
  time to fit residues: 13.2971
Evaluate side-chains
  118 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain R residue  324 LEU
Chi-restraints excluded: chain R residue  366 LEU
Chi-restraints excluded: chain R residue  485 LEU
Chi-restraints excluded: chain R residue  503 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 72 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0670
   chunk 10 optimal weight:    6.9990
   chunk 45 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 34 optimal weight:    8.9990
   overall best weight:    1.3320

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

Flipped N/Q/H residues before XYZ refinement:
R 266 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.166377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.128214 restraints weight = 11980.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 3.25
r_work: 0.3306 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3305
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3305
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   7168  Z= 0.146
  Angle     :  0.580  12.482   9715  Z= 0.296
  Chirality :  0.042   0.149   1110
  Planarity :  0.003   0.038   1201
  Dihedral  :  5.992  49.953   1269
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 17.28 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.30), residues: 867
  helix:  2.63 (0.28), residues: 359
  sheet: -1.55 (0.38), residues: 182
  loop : -1.53 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  19 
 TYR   0.008   0.001   TYR B  59 
 PHE   0.027   0.002   PHE B 292 
 TRP   0.011   0.001   TRP R 355 
 HIS   0.008   0.001   HIS R 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 7166)
  covalent geometry    : angle       0.57606 ( 9713)
  SS BOND              : bond        0.00781 (    1)
  SS BOND              : angle       4.46837 (    2)
  hydrogen bonds       : bond        0.03748 (  340)
  hydrogen bonds       : angle       3.70431 ( 1000)
  Misc. bond           : bond        0.00032 (    1)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.8132 (m-40) cc_final: 0.7590 (t0)
REVERT: A  244 MET cc_start: 0.8684 (tpp) cc_final: 0.8036 (tpp)
REVERT: B  170 ASP cc_start: 0.8460 (t70) cc_final: 0.8088 (t0)
REVERT: B  219 ARG cc_start: 0.8119 (mtt-85) cc_final: 0.7663 (mtt-85)
REVERT: B  228 ASP cc_start: 0.8637 (m-30) cc_final: 0.8023 (m-30)
REVERT: B  234 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8379 (m-80)
REVERT: G   48 ASP cc_start: 0.8194 (t0) cc_final: 0.7808 (t70)
REVERT: R  414 ARG cc_start: 0.5695 (tpt170) cc_final: 0.5010 (mmm-85)
  outliers start: 15
  outliers final: 11
  residues processed: 116
  average time/residue: 0.0801
  time to fit residues: 12.6060
Evaluate side-chains
  115 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain R residue  324 LEU
Chi-restraints excluded: chain R residue  366 LEU
Chi-restraints excluded: chain R residue  485 LEU
Chi-restraints excluded: chain R residue  503 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9980
   chunk 84 optimal weight:    0.0050
   chunk 26 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0670
   chunk 33 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 68 optimal weight:    0.5980
   overall best weight:    0.5132

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

Flipped N/Q/H residues before XYZ refinement:
R 266 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.170041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.130639 restraints weight = 20070.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 5.66
r_work: 0.3238 rms_B_bonded: 5.29 restraints_weight: 2.0000
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3242
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3242
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.066   7168  Z= 0.105
  Angle     :  0.553  12.449   9715  Z= 0.282
  Chirality :  0.040   0.148   1110
  Planarity :  0.003   0.037   1201
  Dihedral  :  5.707  52.138   1269
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 17.55 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.31), residues: 867
  helix:  2.80 (0.28), residues: 359
  sheet: -1.47 (0.38), residues: 182
  loop : -1.47 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  19 
 TYR   0.009   0.001   TYR R 290 
 PHE   0.020   0.001   PHE R 292 
 TRP   0.011   0.001   TRP R 339 
 HIS   0.012   0.001   HIS R 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 7166)
  covalent geometry    : angle       0.55054 ( 9713)
  SS BOND              : bond        0.00728 (    1)
  SS BOND              : angle       3.69338 (    2)
  hydrogen bonds       : bond        0.03261 (  340)
  hydrogen bonds       : angle       3.52901 ( 1000)
  Misc. bond           : bond        0.00004 (    1)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ASN cc_start: 0.8104 (m-40) cc_final: 0.7614 (t0)
REVERT: A  244 MET cc_start: 0.8705 (tpp) cc_final: 0.8045 (tpp)
REVERT: B  170 ASP cc_start: 0.8531 (t70) cc_final: 0.8167 (t0)
REVERT: B  219 ARG cc_start: 0.8213 (mtt-85) cc_final: 0.7725 (mtt-85)
REVERT: B  228 ASP cc_start: 0.8716 (m-30) cc_final: 0.8118 (m-30)
REVERT: B  234 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8305 (m-80)
REVERT: B  243 THR cc_start: 0.7717 (p) cc_final: 0.7466 (p)
REVERT: G   48 ASP cc_start: 0.8221 (t0) cc_final: 0.7935 (t0)
REVERT: R  326 ASN cc_start: 0.8547 (m-40) cc_final: 0.8275 (m-40)
REVERT: R  414 ARG cc_start: 0.5669 (tpt170) cc_final: 0.4913 (mmm-85)
  outliers start: 15
  outliers final: 11
  residues processed: 126
  average time/residue: 0.0783
  time to fit residues: 13.4220
Evaluate side-chains
  120 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue  324 LEU
Chi-restraints excluded: chain R residue  366 LEU
Chi-restraints excluded: chain R residue  485 LEU
Chi-restraints excluded: chain R residue  503 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 9 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 58 optimal weight:    0.2980
   chunk 84 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0870
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A 194 ASN
A 307 GLN
R 266 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.170954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.133131 restraints weight = 9975.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 2.86
r_work: 0.3356 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3362
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3362 r_free = 0.3362    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3362 r_free = 0.3362    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3362
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   7168  Z= 0.111
  Angle     :  0.562  12.514   9715  Z= 0.286
  Chirality :  0.041   0.149   1110
  Planarity :  0.003   0.038   1201
  Dihedral  :  5.668  51.105   1269
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 17.96 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.31), residues: 867
  helix:  2.83 (0.28), residues: 359
  sheet: -1.36 (0.38), residues: 181
  loop : -1.49 (0.35), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  19 
 TYR   0.009   0.001   TYR R 290 
 PHE   0.020   0.001   PHE R 292 
 TRP   0.009   0.001   TRP R 355 
 HIS   0.013   0.001   HIS R 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 7166)
  covalent geometry    : angle       0.55926 ( 9713)
  SS BOND              : bond        0.00709 (    1)
  SS BOND              : angle       3.63809 (    2)
  hydrogen bonds       : bond        0.03278 (  340)
  hydrogen bonds       : angle       3.51123 ( 1000)
  Misc. bond           : bond        0.00012 (    1)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.8063 (m-40) cc_final: 0.7596 (t0)
REVERT: A  246 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7368 (mp0)
REVERT: B   20 ASP cc_start: 0.8609 (m-30) cc_final: 0.8406 (m-30)
REVERT: B  170 ASP cc_start: 0.8471 (t70) cc_final: 0.8128 (t0)
REVERT: B  219 ARG cc_start: 0.8115 (mtt-85) cc_final: 0.7654 (mtt-85)
REVERT: B  228 ASP cc_start: 0.8582 (m-30) cc_final: 0.8039 (m-30)
REVERT: B  234 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8357 (m-80)
REVERT: B  292 PHE cc_start: 0.7591 (m-80) cc_final: 0.7159 (m-80)
REVERT: G   48 ASP cc_start: 0.8198 (t0) cc_final: 0.7838 (t70)
REVERT: R  326 ASN cc_start: 0.8591 (m-40) cc_final: 0.8371 (m-40)
REVERT: R  414 ARG cc_start: 0.5687 (tpt170) cc_final: 0.4944 (mmm-85)
  outliers start: 14
  outliers final: 10
  residues processed: 122
  average time/residue: 0.0710
  time to fit residues: 11.9645
Evaluate side-chains
  122 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue  324 LEU
Chi-restraints excluded: chain R residue  366 LEU
Chi-restraints excluded: chain R residue  485 LEU
Chi-restraints excluded: chain R residue  503 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0060
   chunk 0 optimal weight:   10.0000
   chunk 76 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 14 optimal weight:    8.9990
   chunk 8 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 22 optimal weight:    9.9990
   overall best weight:    1.3400

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

Flipped N/Q/H residues before XYZ refinement:
R 266 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.166590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.127241 restraints weight = 21062.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 6.01
r_work: 0.3177 rms_B_bonded: 5.43 restraints_weight: 2.0000
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3173
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3173
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   7168  Z= 0.150
  Angle     :  0.597  12.336   9715  Z= 0.303
  Chirality :  0.042   0.150   1110
  Planarity :  0.003   0.038   1201
  Dihedral  :  5.950  52.707   1269
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 17.96 %
    Favored  : 80.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.31), residues: 867
  helix:  2.73 (0.28), residues: 359
  sheet: -1.44 (0.38), residues: 182
  loop : -1.48 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  19 
 TYR   0.008   0.001   TYR B  59 
 PHE   0.019   0.001   PHE B 241 
 TRP   0.011   0.001   TRP R 355 
 HIS   0.012   0.001   HIS R 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 7166)
  covalent geometry    : angle       0.59476 ( 9713)
  SS BOND              : bond        0.00718 (    1)
  SS BOND              : angle       3.98908 (    2)
  hydrogen bonds       : bond        0.03758 (  340)
  hydrogen bonds       : angle       3.65416 ( 1000)
  Misc. bond           : bond        0.00038 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1916.86 seconds
wall clock time: 33 minutes 29.93 seconds (2009.93 seconds total)