Starting phenix.real_space_refine
on Wed Mar 12 06:43:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7d76_30602/03_2025/7d76_30602.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7d76_30602/03_2025/7d76_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7d76_30602/03_2025/7d76_30602.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7d76_30602/03_2025/7d76_30602.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7d76_30602/03_2025/7d76_30602.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7d76_30602/03_2025/7d76_30602.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.37, per 1000 atoms: 0.77
  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: 2.12
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.74
  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: 1.88

  Time building geometry restraints manager: 2.23 seconds

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

  Histogram of bond lengths:
        1.19 -     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:             0.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     20.320
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.180
-------------------------------------------------------------------------------
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   7166  Z= 0.517
  Angle     :  0.787   9.350   9713  Z= 0.404
  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 : 8.33
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.55 (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
 TRP   0.016   0.002   TRP B 332 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.018   0.001   PHE R 345 
 TYR   0.035   0.002   TYR B 105 
 ARG   0.005   0.000   ARG B   8 

*********************** 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  : 0.691 
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: 0.2504
  time to fit residues: 41.8860
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  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 35 optimal weight:    4.9990
   chunk 22 optimal weight:    9.9990
   chunk 43 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 66 optimal weight:    8.9990
   chunk 25 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.3898 r_free = 0.3898 target = 0.162149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.124102 restraints weight = 17193.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 4.52
r_work: 0.3196 rms_B_bonded: 4.59 restraints_weight: 0.5000
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3203
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3203
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.1331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7166  Z= 0.189
  Angle     :  0.584  12.411   9713  Z= 0.294
  Chirality :  0.042   0.191   1110
  Planarity :  0.004   0.043   1201
  Dihedral  :  7.977  57.857   1269
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  9.93 %
    Favored  : 88.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.28), residues: 867
  helix:  1.65 (0.27), residues: 352
  sheet: -2.43 (0.36), residues: 172
  loop : -2.19 (0.30), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 339 
 HIS   0.004   0.001   HIS B 311 
 PHE   0.018   0.001   PHE R 292 
 TYR   0.019   0.001   TYR B 105 
 ARG   0.009   0.001   ARG R 411 

*********************** 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
  128 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 ASP cc_start: 0.8022 (t0) cc_final: 0.7789 (t0)
REVERT: A  244 MET cc_start: 0.8708 (tpp) cc_final: 0.8102 (tpp)
REVERT: A  246 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7393 (mp0)
REVERT: A  277 GLU cc_start: 0.8811 (tp30) cc_final: 0.8530 (tp30)
REVERT: A  316 ASN cc_start: 0.8110 (t0) cc_final: 0.7903 (t0)
REVERT: B  170 ASP cc_start: 0.8489 (t70) cc_final: 0.8203 (t0)
REVERT: B  184 THR cc_start: 0.8981 (m) cc_final: 0.8724 (p)
REVERT: B  219 ARG cc_start: 0.8062 (mtt-85) cc_final: 0.7486 (mtt-85)
REVERT: B  228 ASP cc_start: 0.8669 (m-30) cc_final: 0.8254 (m-30)
REVERT: B  241 PHE cc_start: 0.9203 (p90) cc_final: 0.8903 (p90)
REVERT: G   48 ASP cc_start: 0.8092 (t0) cc_final: 0.7717 (t70)
REVERT: R  326 ASN cc_start: 0.8633 (m-40) cc_final: 0.8396 (m-40)
  outliers start: 10
  outliers final: 5
  residues processed: 124
  average time/residue: 0.1997
  time to fit residues: 32.9415
Evaluate side-chains
  114 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 109
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
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 62 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9990
   chunk 35 optimal weight:    6.9990
   chunk 22 optimal weight:    8.9990
   chunk 55 optimal weight:   10.0000
   chunk 70 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 78 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.5384

-------------------------------------------------------------------------------
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 110 ASN
R 266 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.164331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.125156 restraints weight = 17141.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 4.72
r_work: 0.3202 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3193
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3193
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7166  Z= 0.256
  Angle     :  0.582  12.383   9713  Z= 0.295
  Chirality :  0.043   0.175   1110
  Planarity :  0.003   0.038   1201
  Dihedral  :  6.913  54.348   1269
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 13.33 %
    Favored  : 85.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.29), residues: 867
  helix:  2.12 (0.27), residues: 353
  sheet: -2.14 (0.37), residues: 175
  loop : -1.95 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 355 
 HIS   0.002   0.001   HIS B 142 
 PHE   0.016   0.001   PHE R 345 
 TYR   0.012   0.001   TYR B 105 
 ARG   0.005   0.000   ARG R 411 

*********************** 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
  127 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.714 
Fit side-chains
REVERT: A   42 ASP cc_start: 0.8131 (t0) cc_final: 0.7872 (t0)
REVERT: A  244 MET cc_start: 0.8715 (tpp) cc_final: 0.8089 (tpp)
REVERT: A  277 GLU cc_start: 0.8863 (tp30) cc_final: 0.8540 (tp30)
REVERT: A  316 ASN cc_start: 0.8214 (t0) cc_final: 0.7803 (t0)
REVERT: B  170 ASP cc_start: 0.8487 (t70) cc_final: 0.8193 (t0)
REVERT: B  184 THR cc_start: 0.8996 (m) cc_final: 0.8727 (p)
REVERT: B  219 ARG cc_start: 0.8085 (mtt-85) cc_final: 0.7531 (mtt-85)
REVERT: B  228 ASP cc_start: 0.8737 (m-30) cc_final: 0.8189 (m-30)
REVERT: B  241 PHE cc_start: 0.9176 (p90) cc_final: 0.8897 (p90)
REVERT: G   48 ASP cc_start: 0.8099 (t0) cc_final: 0.7625 (t70)
  outliers start: 12
  outliers final: 7
  residues processed: 121
  average time/residue: 0.1780
  time to fit residues: 29.3719
Evaluate side-chains
  112 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
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  315 VAL
Chi-restraints excluded: chain R residue  324 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 48 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 84 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.5984

-------------------------------------------------------------------------------
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 = 0.3939 r_free = 0.3939 target = 0.165544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.125453 restraints weight = 17180.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 4.42
r_work: 0.3229 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3216
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3216
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7166  Z= 0.256
  Angle     :  0.578  12.338   9713  Z= 0.293
  Chirality :  0.043   0.174   1110
  Planarity :  0.003   0.038   1201
  Dihedral  :  6.555  53.369   1269
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 14.15 %
    Favored  : 83.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.30), residues: 867
  helix:  2.31 (0.27), residues: 356
  sheet: -1.97 (0.38), residues: 177
  loop : -1.92 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 355 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.015   0.001   PHE R 345 
 TYR   0.012   0.001   TYR B 105 
 ARG   0.006   0.000   ARG B  19 

*********************** 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
  132 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.699 
Fit side-chains
REVERT: A   42 ASP cc_start: 0.8121 (t0) cc_final: 0.7887 (t0)
REVERT: A  277 GLU cc_start: 0.8862 (tp30) cc_final: 0.8605 (tp30)
REVERT: B  170 ASP cc_start: 0.8525 (t70) cc_final: 0.8203 (t0)
REVERT: B  219 ARG cc_start: 0.8140 (mtt-85) cc_final: 0.7782 (mtt-85)
REVERT: B  228 ASP cc_start: 0.8726 (m-30) cc_final: 0.8229 (m-30)
REVERT: B  234 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8385 (m-80)
REVERT: B  241 PHE cc_start: 0.9162 (p90) cc_final: 0.8887 (p90)
REVERT: R  414 ARG cc_start: 0.5714 (tpt170) cc_final: 0.5030 (mmm-85)
  outliers start: 17
  outliers final: 10
  residues processed: 126
  average time/residue: 0.1854
  time to fit residues: 31.7752
Evaluate side-chains
  119 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
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  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  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 17 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 41 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 22 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 68 optimal weight:    0.0870
   overall best weight:    1.3962

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.166282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.127290 restraints weight = 19137.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 5.19
r_work: 0.3186 rms_B_bonded: 5.13 restraints_weight: 2.0000
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3196
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3196
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7166  Z= 0.234
  Angle     :  0.566  12.471   9713  Z= 0.288
  Chirality :  0.042   0.156   1110
  Planarity :  0.003   0.041   1201
  Dihedral  :  6.328  52.962   1269
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.24 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.30), residues: 867
  helix:  2.40 (0.28), residues: 358
  sheet: -1.83 (0.38), residues: 174
  loop : -1.79 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 421 
 HIS   0.002   0.001   HIS B 142 
 PHE   0.013   0.001   PHE R 345 
 TYR   0.009   0.001   TYR B 105 
 ARG   0.004   0.000   ARG A 349 

*********************** 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
  127 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.766 
Fit side-chains
REVERT: A  244 MET cc_start: 0.8811 (tpp) cc_final: 0.8196 (tpp)
REVERT: A  280 LYS cc_start: 0.8694 (mtmm) cc_final: 0.8301 (ptpp)
REVERT: A  281 LYS cc_start: 0.8991 (mmmt) cc_final: 0.8713 (mmmt)
REVERT: A  291 TYR cc_start: 0.6522 (t80) cc_final: 0.6291 (t80)
REVERT: B  170 ASP cc_start: 0.8555 (t70) cc_final: 0.8233 (t0)
REVERT: B  219 ARG cc_start: 0.8173 (mtt-85) cc_final: 0.7810 (mtt-85)
REVERT: B  228 ASP cc_start: 0.8764 (m-30) cc_final: 0.8264 (m-30)
REVERT: B  234 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8376 (m-80)
REVERT: G   48 ASP cc_start: 0.8237 (t0) cc_final: 0.7751 (t70)
REVERT: R  414 ARG cc_start: 0.5738 (tpt170) cc_final: 0.5018 (mmm-85)
  outliers start: 16
  outliers final: 12
  residues processed: 122
  average time/residue: 0.1730
  time to fit residues: 28.9971
Evaluate side-chains
  122 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
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  178 THR
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  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 56 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0020
   chunk 37 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0670
   chunk 71 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0670
   chunk 49 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.3264

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

Flipped N/Q/H residues before XYZ refinement:
B  54 HIS
R 266 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.170111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.131501 restraints weight = 21027.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 6.05
r_work: 0.3239 rms_B_bonded: 5.50 restraints_weight: 2.0000
r_work (final): 0.3239
-------------------------------------------------------------------------------
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 = 0.45   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: 0.7839
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   7166  Z= 0.138
  Angle     :  0.530  12.762   9713  Z= 0.268
  Chirality :  0.040   0.147   1110
  Planarity :  0.003   0.044   1201
  Dihedral  :  5.787  54.265   1269
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.83 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.30), residues: 867
  helix:  2.75 (0.28), residues: 357
  sheet: -1.66 (0.38), residues: 182
  loop : -1.57 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 339 
 HIS   0.002   0.000   HIS B 142 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.008   0.001   TYR R 290 
 ARG   0.006   0.000   ARG A 349 

*********************** 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
  141 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 0.687 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.8176 (m-40) cc_final: 0.7549 (t0)
REVERT: A  246 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7429 (mp0)
REVERT: A  280 LYS cc_start: 0.8629 (mtmm) cc_final: 0.8427 (ptpp)
REVERT: A  281 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8780 (mmmt)
REVERT: A  316 ASN cc_start: 0.8138 (t0) cc_final: 0.7935 (t0)
REVERT: B  170 ASP cc_start: 0.8598 (t70) cc_final: 0.8275 (t0)
REVERT: B  219 ARG cc_start: 0.8216 (mtt-85) cc_final: 0.7912 (mtt-85)
REVERT: B  228 ASP cc_start: 0.8691 (m-30) cc_final: 0.8089 (m-30)
REVERT: B  234 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8335 (m-80)
REVERT: B  256 ARG cc_start: 0.8548 (mtm-85) cc_final: 0.8299 (mtp180)
REVERT: G   48 ASP cc_start: 0.8244 (t0) cc_final: 0.7940 (t0)
REVERT: R  326 ASN cc_start: 0.8572 (m-40) cc_final: 0.8322 (m-40)
REVERT: R  414 ARG cc_start: 0.5642 (tpt170) cc_final: 0.4890 (mmm-85)
  outliers start: 19
  outliers final: 8
  residues processed: 135
  average time/residue: 0.1908
  time to fit residues: 34.7908
Evaluate side-chains
  123 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 114
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   37 ILE
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 42 optimal weight:    0.0980
   chunk 39 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 56 optimal weight:    8.9990
   chunk 62 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 46 optimal weight:    0.4980
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3931 r_free = 0.3931 target = 0.165477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.127857 restraints weight = 13442.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 3.51
r_work: 0.3292 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3298
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3298 r_free = 0.3298    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3298 r_free = 0.3298    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3298
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.2286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7166  Z= 0.157
  Angle     :  0.539  12.819   9713  Z= 0.274
  Chirality :  0.041   0.150   1110
  Planarity :  0.003   0.049   1201
  Dihedral  :  5.718  51.547   1269
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 16.33 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.30), residues: 867
  helix:  2.76 (0.28), residues: 359
  sheet: -1.46 (0.39), residues: 174
  loop : -1.50 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 266 
 PHE   0.020   0.001   PHE R 292 
 TYR   0.009   0.001   TYR R 290 
 ARG   0.008   0.000   ARG B  19 

*********************** 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
  127 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.787 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.8071 (m-40) cc_final: 0.7515 (t0)
REVERT: A  244 MET cc_start: 0.8772 (tpp) cc_final: 0.8167 (tpp)
REVERT: A  246 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7411 (mp0)
REVERT: A  316 ASN cc_start: 0.8212 (t0) cc_final: 0.7986 (t0)
REVERT: B  170 ASP cc_start: 0.8472 (t70) cc_final: 0.8116 (t0)
REVERT: B  200 VAL cc_start: 0.8793 (m) cc_final: 0.8577 (p)
REVERT: B  219 ARG cc_start: 0.8087 (mtt-85) cc_final: 0.7764 (mtt-85)
REVERT: B  228 ASP cc_start: 0.8498 (m-30) cc_final: 0.7879 (m-30)
REVERT: B  234 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8433 (m-80)
REVERT: G   48 ASP cc_start: 0.8266 (t0) cc_final: 0.7910 (t0)
REVERT: R  326 ASN cc_start: 0.8531 (m-40) cc_final: 0.8276 (m-40)
REVERT: R  414 ARG cc_start: 0.5652 (tpt170) cc_final: 0.4939 (mmm-85)
  outliers start: 13
  outliers final: 10
  residues processed: 124
  average time/residue: 0.1927
  time to fit residues: 32.0874
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  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 75 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 77 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 74 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3920 r_free = 0.3920 target = 0.164363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.119394 restraints weight = 26373.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 5.25
r_work: 0.3187 rms_B_bonded: 5.08 restraints_weight: 2.0000
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3190
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3190
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7166  Z= 0.183
  Angle     :  0.551  12.605   9713  Z= 0.279
  Chirality :  0.041   0.150   1110
  Planarity :  0.003   0.045   1201
  Dihedral  :  5.776  50.051   1269
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 16.60 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.30), residues: 867
  helix:  2.78 (0.28), residues: 359
  sheet: -1.40 (0.39), residues: 174
  loop : -1.49 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.011   0.001   HIS R 266 
 PHE   0.018   0.001   PHE R 292 
 TYR   0.009   0.001   TYR R 290 
 ARG   0.005   0.000   ARG A 349 

*********************** 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
  126 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.718 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.8084 (m-40) cc_final: 0.7489 (t0)
REVERT: A  231 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7856 (m-80)
REVERT: A  244 MET cc_start: 0.8770 (tpp) cc_final: 0.8099 (tpp)
REVERT: A  246 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7340 (mp0)
REVERT: A  316 ASN cc_start: 0.8224 (t0) cc_final: 0.8021 (t0)
REVERT: B  170 ASP cc_start: 0.8473 (t70) cc_final: 0.8076 (t0)
REVERT: B  219 ARG cc_start: 0.8100 (mtt-85) cc_final: 0.7603 (mtt-85)
REVERT: B  228 ASP cc_start: 0.8574 (m-30) cc_final: 0.7956 (m-30)
REVERT: B  234 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8436 (m-80)
REVERT: B  292 PHE cc_start: 0.8170 (m-80) cc_final: 0.7807 (m-80)
REVERT: G   48 ASP cc_start: 0.8298 (t0) cc_final: 0.7978 (t0)
REVERT: R  326 ASN cc_start: 0.8514 (m-40) cc_final: 0.8274 (m-40)
REVERT: R  414 ARG cc_start: 0.5582 (tpt170) cc_final: 0.4858 (mmm-85)
  outliers start: 16
  outliers final: 11
  residues processed: 123
  average time/residue: 0.1715
  time to fit residues: 29.0133
Evaluate side-chains
  122 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 TYR
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 75 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 81 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0050
   chunk 61 optimal weight:    0.6980
   chunk 18 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 52 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.5794

-------------------------------------------------------------------------------
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 = 0.3986 r_free = 0.3986 target = 0.170332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.129944 restraints weight = 15807.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 4.10
r_work: 0.3308 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3310
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3310 r_free = 0.3310    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 = 0.3310 r_free = 0.3310    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3310
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.2454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7166  Z= 0.157
  Angle     :  0.543  12.534   9713  Z= 0.272
  Chirality :  0.040   0.150   1110
  Planarity :  0.003   0.037   1201
  Dihedral  :  5.621  50.707   1269
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 17.96 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.31), residues: 867
  helix:  2.89 (0.28), residues: 359
  sheet: -1.40 (0.39), residues: 182
  loop : -1.46 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 339 
 HIS   0.011   0.001   HIS R 266 
 PHE   0.018   0.001   PHE R 292 
 TYR   0.009   0.001   TYR R 290 
 ARG   0.003   0.000   ARG A 349 

*********************** 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
  129 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.832 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.8061 (m-40) cc_final: 0.7638 (t0)
REVERT: A  231 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7935 (m-80)
REVERT: A  244 MET cc_start: 0.8724 (tpp) cc_final: 0.8094 (tpp)
REVERT: A  246 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7436 (mp0)
REVERT: B  170 ASP cc_start: 0.8495 (t70) cc_final: 0.8108 (t0)
REVERT: B  219 ARG cc_start: 0.8120 (mtt-85) cc_final: 0.7666 (mtt-85)
REVERT: B  228 ASP cc_start: 0.8575 (m-30) cc_final: 0.8007 (m-30)
REVERT: B  234 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8383 (m-80)
REVERT: B  243 THR cc_start: 0.7639 (p) cc_final: 0.7387 (p)
REVERT: B  292 PHE cc_start: 0.7838 (m-80) cc_final: 0.7480 (m-80)
REVERT: G   48 ASP cc_start: 0.8208 (t0) cc_final: 0.7821 (t70)
REVERT: R  326 ASN cc_start: 0.8552 (m-40) cc_final: 0.8283 (m-40)
REVERT: R  414 ARG cc_start: 0.5668 (tpt170) cc_final: 0.4914 (mmm-85)
  outliers start: 11
  outliers final: 8
  residues processed: 126
  average time/residue: 0.1839
  time to fit residues: 31.6507
Evaluate side-chains
  123 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 TYR
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 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 72 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    1.2586

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.167033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.122452 restraints weight = 19609.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 4.59
r_work: 0.3239 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3211
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3211
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   7166  Z= 0.232
  Angle     :  0.592  12.475   9713  Z= 0.303
  Chirality :  0.042   0.150   1110
  Planarity :  0.003   0.038   1201
  Dihedral  :  5.877  51.986   1269
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 18.23 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.30), residues: 867
  helix:  2.73 (0.28), residues: 359
  sheet: -1.46 (0.38), residues: 182
  loop : -1.47 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 355 
 HIS   0.011   0.001   HIS R 266 
 PHE   0.017   0.001   PHE R 292 
 TYR   0.007   0.001   TYR R 290 
 ARG   0.004   0.000   ARG B  19 

********************** 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
  123 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.775 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.8096 (m-40) cc_final: 0.7575 (t0)
REVERT: A  231 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.7958 (m-80)
REVERT: B  170 ASP cc_start: 0.8507 (t70) cc_final: 0.8106 (t0)
REVERT: B  219 ARG cc_start: 0.8142 (mtt-85) cc_final: 0.7697 (mtt-85)
REVERT: B  228 ASP cc_start: 0.8672 (m-30) cc_final: 0.8140 (m-30)
REVERT: B  234 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8383 (m-80)
REVERT: B  292 PHE cc_start: 0.7963 (m-80) cc_final: 0.7596 (m-80)
REVERT: G   48 ASP cc_start: 0.8318 (t0) cc_final: 0.7925 (t70)
REVERT: R  326 ASN cc_start: 0.8649 (m-40) cc_final: 0.8380 (m-40)
REVERT: R  414 ARG cc_start: 0.5702 (tpt170) cc_final: 0.4991 (mmm-85)
  outliers start: 14
  outliers final: 10
  residues processed: 120
  average time/residue: 0.1736
  time to fit residues: 28.7764
Evaluate side-chains
  122 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 TYR
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 76 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   chunk 14 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 22 optimal weight:   10.0000
   chunk 73 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3969 r_free = 0.3969 target = 0.168538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.127701 restraints weight = 17035.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 4.57
r_work: 0.3259 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3265
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3265
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   7166  Z= 0.196
  Angle     :  0.575  12.401   9713  Z= 0.295
  Chirality :  0.041   0.149   1110
  Planarity :  0.003   0.041   1201
  Dihedral  :  5.795  53.034   1269
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 18.10 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.30), residues: 867
  helix:  2.79 (0.28), residues: 359
  sheet: -1.35 (0.39), residues: 174
  loop : -1.47 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 297 
 HIS   0.013   0.001   HIS R 266 
 PHE   0.017   0.001   PHE R 292 
 TYR   0.009   0.001   TYR R 290 
 ARG   0.004   0.000   ARG A 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4166.93 seconds
wall clock time: 72 minutes 10.40 seconds (4330.40 seconds total)