Starting phenix.real_space_refine
on Wed Mar 12 23:38:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7cr2_30445/03_2025/7cr2_30445_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7cr2_30445/03_2025/7cr2_30445.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7cr2_30445/03_2025/7cr2_30445.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7cr2_30445/03_2025/7cr2_30445.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7cr2_30445/03_2025/7cr2_30445_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7cr2_30445/03_2025/7cr2_30445_trim.cif"
  }
  resolution = 3.2
  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=   0.003
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      36      5.16       5
     C    5500      2.51       5
     N    1392      2.21       5
     O    1344      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8276
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2047
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 2047
          Classifications: {'peptide': 251}
          Link IDs: {'PTRANS': 4, 'TRANS': 246}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Unusual residues: {'FBX': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 5.02, per 1000 atoms: 0.61
  Number of scatterers: 8276
  At special positions: 0
  Unit cell: (130.806, 130.806, 75.036, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      36     16.00
     F       4      9.00
     O    1344      8.00
     N    1392      7.00
     C    5500      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.34
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1856

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 0 sheets defined
      85.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 71 through 85
    Processing helix  chain 'A' and resid 91 through 113
      removed outlier: 3.881A  pdb=" N   TYR A  95 " --> pdb=" O   TRP A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 148
      removed outlier: 3.827A  pdb=" N   ILE A 128 " --> pdb=" O   GLY A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 151
      No H-bonds generated for 'chain 'A' and resid 149 through 151'
    Processing helix  chain 'A' and resid 155 through 164
      removed outlier: 3.806A  pdb=" N   GLY A 159 " --> pdb=" O   ARG A 155 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   ALA A 164 " --> pdb=" O   ARG A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 183
      removed outlier: 3.699A  pdb=" N   LEU A 183 " --> pdb=" O   SER A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 210
    Processing helix  chain 'A' and resid 215 through 228
      removed outlier: 3.510A  pdb=" N   HIS A 228 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 254
    Processing helix  chain 'A' and resid 263 through 276
      removed outlier: 3.644A  pdb=" N   THR A 276 " --> pdb=" O   LEU A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 305
      removed outlier: 3.657A  pdb=" N   THR A 296 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LEU A 299 " --> pdb=" O   ALA A 295 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   SER A 303 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 330
    Processing helix  chain 'B' and resid 71 through 85
    Processing helix  chain 'B' and resid 91 through 113
      removed outlier: 3.881A  pdb=" N   TYR B  95 " --> pdb=" O   TRP B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 148
      removed outlier: 3.827A  pdb=" N   ILE B 128 " --> pdb=" O   GLY B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 151
      No H-bonds generated for 'chain 'B' and resid 149 through 151'
    Processing helix  chain 'B' and resid 155 through 164
      removed outlier: 3.806A  pdb=" N   GLY B 159 " --> pdb=" O   ARG B 155 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   ALA B 164 " --> pdb=" O   ARG B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 183
      removed outlier: 3.700A  pdb=" N   LEU B 183 " --> pdb=" O   SER B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 210
    Processing helix  chain 'B' and resid 215 through 228
      removed outlier: 3.511A  pdb=" N   HIS B 228 " --> pdb=" O   VAL B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 254
    Processing helix  chain 'B' and resid 263 through 276
      removed outlier: 3.642A  pdb=" N   THR B 276 " --> pdb=" O   LEU B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 305
      removed outlier: 3.657A  pdb=" N   THR B 296 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU B 299 " --> pdb=" O   ALA B 295 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   SER B 303 " --> pdb=" O   LEU B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 330
    Processing helix  chain 'C' and resid 71 through 85
    Processing helix  chain 'C' and resid 91 through 113
      removed outlier: 3.881A  pdb=" N   TYR C  95 " --> pdb=" O   TRP C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 148
      removed outlier: 3.827A  pdb=" N   ILE C 128 " --> pdb=" O   GLY C 124 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 149 through 151
      No H-bonds generated for 'chain 'C' and resid 149 through 151'
    Processing helix  chain 'C' and resid 155 through 164
      removed outlier: 3.806A  pdb=" N   GLY C 159 " --> pdb=" O   ARG C 155 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   ALA C 164 " --> pdb=" O   ARG C 160 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 166 through 183
      removed outlier: 3.700A  pdb=" N   LEU C 183 " --> pdb=" O   SER C 179 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 210
    Processing helix  chain 'C' and resid 215 through 228
      removed outlier: 3.511A  pdb=" N   HIS C 228 " --> pdb=" O   VAL C 224 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 228 through 254
    Processing helix  chain 'C' and resid 263 through 276
      removed outlier: 3.642A  pdb=" N   THR C 276 " --> pdb=" O   LEU C 272 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 287 through 305
      removed outlier: 3.657A  pdb=" N   THR C 296 " --> pdb=" O   LEU C 292 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU C 299 " --> pdb=" O   ALA C 295 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   SER C 303 " --> pdb=" O   LEU C 299 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 306 through 330
    Processing helix  chain 'D' and resid 71 through 85
    Processing helix  chain 'D' and resid 91 through 113
      removed outlier: 3.881A  pdb=" N   TYR D  95 " --> pdb=" O   TRP D  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 148
      removed outlier: 3.827A  pdb=" N   ILE D 128 " --> pdb=" O   GLY D 124 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 149 through 151
      No H-bonds generated for 'chain 'D' and resid 149 through 151'
    Processing helix  chain 'D' and resid 155 through 164
      removed outlier: 3.806A  pdb=" N   GLY D 159 " --> pdb=" O   ARG D 155 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   ALA D 164 " --> pdb=" O   ARG D 160 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 166 through 183
      removed outlier: 3.700A  pdb=" N   LEU D 183 " --> pdb=" O   SER D 179 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 196 through 210
    Processing helix  chain 'D' and resid 215 through 228
      removed outlier: 3.511A  pdb=" N   HIS D 228 " --> pdb=" O   VAL D 224 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 228 through 254
    Processing helix  chain 'D' and resid 263 through 276
      removed outlier: 3.642A  pdb=" N   THR D 276 " --> pdb=" O   LEU D 272 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 287 through 305
      removed outlier: 3.657A  pdb=" N   THR D 296 " --> pdb=" O   LEU D 292 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU D 299 " --> pdb=" O   ALA D 295 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   SER D 303 " --> pdb=" O   LEU D 299 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 306 through 330

    628 hydrogen bonds defined for protein.
    1884 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.40

  Time building geometry restraints manager: 2.73 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1204
        1.30 -     1.43: 2635
        1.43 -     1.56: 4617
        1.56 -     1.68: 0
        1.68 -     1.81: 48
  Bond restraints: 8504
  Sorted by residual:
  bond pdb=" C17 FBX A 801 "
       pdb=" C19 FBX A 801 "
    ideal  model  delta    sigma   weight residual
    1.381  1.519 -0.138 2.00e-02 2.50e+03 4.78e+01
  bond pdb=" C17 FBX D 801 "
       pdb=" C19 FBX D 801 "
    ideal  model  delta    sigma   weight residual
    1.381  1.519 -0.138 2.00e-02 2.50e+03 4.77e+01
  bond pdb=" C17 FBX C 801 "
       pdb=" C19 FBX C 801 "
    ideal  model  delta    sigma   weight residual
    1.381  1.519 -0.138 2.00e-02 2.50e+03 4.77e+01
  bond pdb=" C17 FBX B 801 "
       pdb=" C19 FBX B 801 "
    ideal  model  delta    sigma   weight residual
    1.381  1.519 -0.138 2.00e-02 2.50e+03 4.77e+01
  bond pdb=" C13 FBX A 801 "
       pdb=" C14 FBX A 801 "
    ideal  model  delta    sigma   weight residual
    1.385  1.510 -0.125 2.00e-02 2.50e+03 3.91e+01
  ... (remaining 8499 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 10842
        1.78 -     3.56: 526
        3.56 -     5.35: 108
        5.35 -     7.13: 8
        7.13 -     8.91: 24
  Bond angle restraints: 11508
  Sorted by residual:
  angle pdb=" CA  TRP A 157 "
        pdb=" CB  TRP A 157 "
        pdb=" CG  TRP A 157 "
      ideal   model   delta    sigma   weight residual
     113.60  118.68   -5.08 1.90e+00 2.77e-01 7.15e+00
  angle pdb=" CA  TRP B 157 "
        pdb=" CB  TRP B 157 "
        pdb=" CG  TRP B 157 "
      ideal   model   delta    sigma   weight residual
     113.60  118.67   -5.07 1.90e+00 2.77e-01 7.11e+00
  angle pdb=" CA  TRP D 157 "
        pdb=" CB  TRP D 157 "
        pdb=" CG  TRP D 157 "
      ideal   model   delta    sigma   weight residual
     113.60  118.67   -5.07 1.90e+00 2.77e-01 7.11e+00
  angle pdb=" CA  TRP C 157 "
        pdb=" CB  TRP C 157 "
        pdb=" CG  TRP C 157 "
      ideal   model   delta    sigma   weight residual
     113.60  118.67   -5.07 1.90e+00 2.77e-01 7.11e+00
  angle pdb=" N5  FBX D 801 "
        pdb=" C20 FBX D 801 "
        pdb=" O2  FBX D 801 "
      ideal   model   delta    sigma   weight residual
     110.60  118.59   -7.99 3.00e+00 1.11e-01 7.09e+00
  ... (remaining 11503 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.33: 4656
       32.33 -    64.65: 132
       64.65 -    96.98: 16
       96.98 -   129.30: 0
      129.30 -   161.63: 4
  Dihedral angle restraints: 4808
    sinusoidal: 1900
      harmonic: 2908
  Sorted by residual:
  dihedral pdb=" C8  FBX A 801 "
           pdb=" C7  FBX A 801 "
           pdb=" N4  FBX A 801 "
           pdb=" C9  FBX A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -75.46   86.17 -161.63     1      3.00e+01 1.11e-03 2.08e+01
  dihedral pdb=" C8  FBX C 801 "
           pdb=" C7  FBX C 801 "
           pdb=" N4  FBX C 801 "
           pdb=" C9  FBX C 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -75.46   86.13 -161.59     1      3.00e+01 1.11e-03 2.08e+01
  dihedral pdb=" C8  FBX B 801 "
           pdb=" C7  FBX B 801 "
           pdb=" N4  FBX B 801 "
           pdb=" C9  FBX B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -75.46   86.13 -161.59     1      3.00e+01 1.11e-03 2.08e+01
  ... (remaining 4805 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 561
       0.030 -    0.060: 452
       0.060 -    0.091: 163
       0.091 -    0.121: 67
       0.121 -    0.151: 9
  Chirality restraints: 1252
  Sorted by residual:
  chirality pdb=" CA  PRO B 308 "
            pdb=" N   PRO B 308 "
            pdb=" C   PRO B 308 "
            pdb=" CB  PRO B 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.69e-01
  chirality pdb=" CA  PRO D 308 "
            pdb=" N   PRO D 308 "
            pdb=" C   PRO D 308 "
            pdb=" CB  PRO D 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.69e-01
  chirality pdb=" CA  PRO C 308 "
            pdb=" N   PRO C 308 "
            pdb=" C   PRO C 308 "
            pdb=" CB  PRO C 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.69e-01
  ... (remaining 1249 not shown)

  Planarity restraints: 1392
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 127 "   -0.016 2.00e-02 2.50e+03   1.13e-02 2.54e+00
        pdb=" CG  TYR A 127 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 127 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 127 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 127 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 127 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 127 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 127 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 127 "    0.016 2.00e-02 2.50e+03   1.12e-02 2.49e+00
        pdb=" CG  TYR D 127 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 127 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 127 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 127 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 127 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 127 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR D 127 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 127 "    0.016 2.00e-02 2.50e+03   1.12e-02 2.49e+00
        pdb=" CG  TYR C 127 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 127 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 127 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 127 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 127 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 127 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR C 127 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1389 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 108
        2.62 -     3.19: 8506
        3.19 -     3.76: 12605
        3.76 -     4.33: 17723
        4.33 -     4.90: 27825
  Nonbonded interactions: 66767
  Sorted by model distance:
  nonbonded pdb=" O   LEU C 107 "
            pdb=" OG  SER C 110 "
     model   vdw
     2.052 3.040
  nonbonded pdb=" O   LEU B 107 "
            pdb=" OG  SER B 110 "
     model   vdw
     2.052 3.040
  nonbonded pdb=" O   LEU D 107 "
            pdb=" OG  SER D 110 "
     model   vdw
     2.052 3.040
  nonbonded pdb=" O   LEU A 107 "
            pdb=" OG  SER A 110 "
     model   vdw
     2.053 3.040
  nonbonded pdb=" O   LEU C 176 "
            pdb=" OG  SER C 179 "
     model   vdw
     2.255 3.040
  ... (remaining 66762 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.330
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.740
  Find NCS groups from input model:        0.170
  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:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
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      :  0.014   0.138   8504  Z= 0.917
  Angle     :  0.977   8.909  11508  Z= 0.510
  Chirality :  0.048   0.151   1252
  Planarity :  0.004   0.020   1392
  Dihedral  : 16.204 161.628   2952
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 39.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  9.17 %
    Favored  : 90.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.81 (0.23), residues: 988
  helix: -1.64 (0.15), residues: 776
  sheet:  None (None), residues: 0
  loop : -1.88 (0.47), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP C 157 
 HIS   0.004   0.002   HIS C  96 
 PHE   0.022   0.003   PHE A 297 
 TYR   0.027   0.003   TYR A 127 
 ARG   0.008   0.001   ARG B 201 

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 148
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 MET cc_start: 0.1887 (ttp) cc_final: 0.1496 (tmm)
REVERT: B  174 MET cc_start: 0.1883 (ttp) cc_final: 0.1501 (tmm)
REVERT: C  174 MET cc_start: 0.1872 (ttp) cc_final: 0.1495 (tmm)
REVERT: D  174 MET cc_start: 0.1874 (ttp) cc_final: 0.1496 (tmm)
  outliers start: 4
  outliers final: 0
  residues processed: 148
  average time/residue: 0.3409
  time to fit residues: 61.7955
Evaluate side-chains
  120 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 75 optimal weight:    9.9990
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    9.9990
   chunk 51 optimal weight:    9.9990
   chunk 40 optimal weight:    0.8980
   chunk 78 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 58 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A  78 GLN
A 228 HIS
B  78 GLN
B 228 HIS
C  78 GLN
C 228 HIS
D  78 GLN
D 228 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.196788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.128627 restraints weight = 10746.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 1.98
r_work: 0.3357 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   8504  Z= 0.263
  Angle     :  0.595   5.616  11508  Z= 0.319
  Chirality :  0.040   0.130   1252
  Planarity :  0.004   0.034   1392
  Dihedral  : 11.139 158.895   1140
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 16.31 %
    Favored  : 81.55 %
  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: -0.12 (0.26), residues: 988
  helix:  0.46 (0.17), residues: 820
  sheet:  None (None), residues: 0
  loop : -2.45 (0.47), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 157 
 HIS   0.002   0.001   HIS A 324 
 PHE   0.015   0.002   PHE B 316 
 TYR   0.024   0.002   TYR D  82 
 ARG   0.005   0.001   ARG A 207 

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 144
  time to evaluate  : 0.855 
Fit side-chains
REVERT: A  162 LYS cc_start: 0.5621 (ptmt) cc_final: 0.5342 (pttp)
  outliers start: 18
  outliers final: 18
  residues processed: 162
  average time/residue: 0.3385
  time to fit residues: 69.5047
Evaluate side-chains
  135 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 CYS
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  242 CYS
Chi-restraints excluded: chain B residue  244 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  242 CYS
Chi-restraints excluded: chain C residue  244 ILE
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  298 THR
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  242 CYS
Chi-restraints excluded: chain D residue  244 ILE
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  298 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   chunk 86 optimal weight:    0.9990
   chunk 95 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A  83 ASN
B  83 ASN
C  83 ASN
D  83 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.198457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.131237 restraints weight = 10839.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 1.97
r_work: 0.3379 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.3261 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.3067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8504  Z= 0.220
  Angle     :  0.527   5.882  11508  Z= 0.282
  Chirality :  0.038   0.119   1252
  Planarity :  0.004   0.043   1392
  Dihedral  : 10.916 157.317   1140
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 17.50 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.27), residues: 988
  helix:  1.28 (0.18), residues: 824
  sheet:  None (None), residues: 0
  loop : -2.80 (0.42), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 157 
 HIS   0.001   0.001   HIS B 324 
 PHE   0.016   0.002   PHE A 316 
 TYR   0.014   0.002   TYR B 141 
 ARG   0.005   0.000   ARG D 207 

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 123
  time to evaluate  : 0.877 
Fit side-chains
REVERT: B   86 GLU cc_start: 0.6798 (tp30) cc_final: 0.6594 (tp30)
REVERT: C   86 GLU cc_start: 0.6799 (tp30) cc_final: 0.6593 (tp30)
REVERT: D   86 GLU cc_start: 0.6812 (tp30) cc_final: 0.6605 (tp30)
  outliers start: 30
  outliers final: 18
  residues processed: 149
  average time/residue: 0.2965
  time to fit residues: 56.1434
Evaluate side-chains
  137 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  244 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  244 ILE
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  244 ILE
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  320 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 93 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 33 optimal weight:   20.0000
   chunk 73 optimal weight:    0.9990
   chunk 50 optimal weight:   10.0000
   chunk 95 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    1.1784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.198571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.130904 restraints weight = 10746.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 2.01
r_work: 0.3382 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.3480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8504  Z= 0.216
  Angle     :  0.529   6.622  11508  Z= 0.281
  Chirality :  0.038   0.142   1252
  Planarity :  0.003   0.039   1392
  Dihedral  : 10.863 156.243   1140
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 18.57 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.27), residues: 988
  helix:  1.68 (0.18), residues: 828
  sheet:  None (None), residues: 0
  loop : -2.97 (0.40), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 157 
 HIS   0.002   0.001   HIS A 324 
 PHE   0.017   0.002   PHE A 137 
 TYR   0.014   0.001   TYR B  74 
 ARG   0.005   0.001   ARG A 207 

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 128
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 GLU cc_start: 0.6794 (tp30) cc_final: 0.6571 (tp30)
REVERT: A  117 GLU cc_start: 0.5452 (pt0) cc_final: 0.5221 (pt0)
REVERT: B  162 LYS cc_start: 0.5447 (pttp) cc_final: 0.5181 (pttp)
REVERT: C  162 LYS cc_start: 0.5458 (pttp) cc_final: 0.5190 (pttp)
REVERT: D  162 LYS cc_start: 0.5463 (pttp) cc_final: 0.5197 (pttp)
  outliers start: 27
  outliers final: 22
  residues processed: 154
  average time/residue: 0.2779
  time to fit residues: 54.4749
Evaluate side-chains
  143 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  244 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  244 ILE
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  244 ILE
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  320 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 78 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 96 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.8984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.198701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.130669 restraints weight = 10687.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 1.99
r_work: 0.3393 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.3275 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.3732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   8504  Z= 0.178
  Angle     :  0.497   5.550  11508  Z= 0.262
  Chirality :  0.037   0.117   1252
  Planarity :  0.003   0.018   1392
  Dihedral  : 10.782 155.464   1140
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 19.40 %
    Favored  : 77.02 %
  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:  1.85 (0.27), residues: 988
  helix:  1.97 (0.18), residues: 828
  sheet:  None (None), residues: 0
  loop : -2.94 (0.40), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 157 
 HIS   0.002   0.001   HIS A 324 
 PHE   0.014   0.001   PHE A 137 
 TYR   0.012   0.001   TYR B  74 
 ARG   0.004   0.000   ARG A  87 

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 129
  time to evaluate  : 0.909 
Fit side-chains
REVERT: A   87 ARG cc_start: 0.7201 (tpp80) cc_final: 0.6946 (tpp80)
REVERT: A  328 HIS cc_start: 0.6266 (OUTLIER) cc_final: 0.5351 (t-90)
REVERT: B  162 LYS cc_start: 0.5444 (pttp) cc_final: 0.5222 (pttp)
REVERT: B  328 HIS cc_start: 0.6291 (OUTLIER) cc_final: 0.5404 (t-90)
REVERT: C  162 LYS cc_start: 0.5444 (pttp) cc_final: 0.5219 (pttp)
REVERT: C  328 HIS cc_start: 0.6289 (OUTLIER) cc_final: 0.5418 (t-90)
REVERT: D  162 LYS cc_start: 0.5450 (pttp) cc_final: 0.5226 (pttp)
REVERT: D  328 HIS cc_start: 0.6280 (OUTLIER) cc_final: 0.5407 (t-90)
  outliers start: 30
  outliers final: 23
  residues processed: 155
  average time/residue: 0.2607
  time to fit residues: 52.2148
Evaluate side-chains
  149 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 122
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  328 HIS
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  244 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  328 HIS
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  173 ILE
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  244 ILE
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain C residue  328 HIS
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  173 ILE
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  244 ILE
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  320 VAL
Chi-restraints excluded: chain D residue  328 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 7 optimal weight:    0.0020
   chunk 83 optimal weight:   20.0000
   chunk 6 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 72 optimal weight:    0.6980
   chunk 66 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.6188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.200831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.132994 restraints weight = 10697.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 1.99
r_work: 0.3424 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.4083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8504  Z= 0.153
  Angle     :  0.476   5.994  11508  Z= 0.251
  Chirality :  0.035   0.108   1252
  Planarity :  0.003   0.021   1392
  Dihedral  : 10.664 155.214   1140
  Min Nonbonded Distance : 2.651

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 20.00 %
    Favored  : 77.02 %
  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:  2.13 (0.27), residues: 988
  helix:  2.15 (0.18), residues: 832
  sheet:  None (None), residues: 0
  loop : -2.89 (0.39), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 157 
 HIS   0.002   0.001   HIS A 324 
 PHE   0.010   0.001   PHE A 240 
 TYR   0.011   0.001   TYR A  74 
 ARG   0.003   0.000   ARG A  87 

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 0.840 
Fit side-chains
REVERT: A  123 GLU cc_start: 0.6113 (OUTLIER) cc_final: 0.5209 (pt0)
REVERT: A  328 HIS cc_start: 0.6484 (OUTLIER) cc_final: 0.5467 (t-90)
REVERT: B  123 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5122 (pt0)
REVERT: B  162 LYS cc_start: 0.5417 (pttp) cc_final: 0.5210 (pttp)
REVERT: B  328 HIS cc_start: 0.6488 (OUTLIER) cc_final: 0.5483 (t-90)
REVERT: C  123 GLU cc_start: 0.5999 (OUTLIER) cc_final: 0.5119 (pt0)
REVERT: C  162 LYS cc_start: 0.5429 (pttp) cc_final: 0.5219 (pttp)
REVERT: C  328 HIS cc_start: 0.6488 (OUTLIER) cc_final: 0.5493 (t-90)
REVERT: D  123 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.5132 (pt0)
REVERT: D  162 LYS cc_start: 0.5437 (pttp) cc_final: 0.5225 (pttp)
REVERT: D  328 HIS cc_start: 0.6483 (OUTLIER) cc_final: 0.5486 (t-90)
  outliers start: 25
  outliers final: 17
  residues processed: 146
  average time/residue: 0.2675
  time to fit residues: 50.0486
Evaluate side-chains
  139 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 114
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  328 HIS
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  123 GLU
Chi-restraints excluded: chain B residue  244 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  328 HIS
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  123 GLU
Chi-restraints excluded: chain C residue  244 ILE
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain C residue  328 HIS
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  123 GLU
Chi-restraints excluded: chain D residue  244 ILE
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  320 VAL
Chi-restraints excluded: chain D residue  328 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:    9.9990
   chunk 80 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 92 optimal weight:    0.6980
   overall best weight:    1.0184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.198993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.131039 restraints weight = 10656.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 1.98
r_work: 0.3395 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.3276 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.4063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   8504  Z= 0.188
  Angle     :  0.500   6.521  11508  Z= 0.261
  Chirality :  0.037   0.115   1252
  Planarity :  0.003   0.024   1392
  Dihedral  : 10.682 154.969   1140
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 17.50 %
    Favored  : 77.02 %
  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:  2.13 (0.27), residues: 988
  helix:  2.18 (0.18), residues: 828
  sheet:  None (None), residues: 0
  loop : -2.95 (0.38), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 146 
 HIS   0.001   0.000   HIS A 324 
 PHE   0.016   0.001   PHE A 137 
 TYR   0.013   0.001   TYR A  82 
 ARG   0.004   0.000   ARG A 207 

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 123
  time to evaluate  : 0.973 
Fit side-chains
REVERT: A  123 GLU cc_start: 0.6098 (OUTLIER) cc_final: 0.5213 (pt0)
REVERT: A  328 HIS cc_start: 0.6572 (OUTLIER) cc_final: 0.5417 (t-90)
REVERT: B  123 GLU cc_start: 0.6010 (OUTLIER) cc_final: 0.5117 (pt0)
REVERT: B  162 LYS cc_start: 0.5548 (pttp) cc_final: 0.5326 (pttp)
REVERT: B  328 HIS cc_start: 0.6519 (OUTLIER) cc_final: 0.5390 (t-90)
REVERT: C  123 GLU cc_start: 0.6014 (OUTLIER) cc_final: 0.5124 (pt0)
REVERT: C  162 LYS cc_start: 0.5565 (pttp) cc_final: 0.5342 (pttp)
REVERT: C  328 HIS cc_start: 0.6573 (OUTLIER) cc_final: 0.5452 (t-90)
REVERT: D  123 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.5129 (pt0)
REVERT: D  162 LYS cc_start: 0.5556 (pttp) cc_final: 0.5326 (pttp)
REVERT: D  328 HIS cc_start: 0.6572 (OUTLIER) cc_final: 0.5441 (t-90)
  outliers start: 46
  outliers final: 33
  residues processed: 163
  average time/residue: 0.2532
  time to fit residues: 53.9910
Evaluate side-chains
  162 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 121
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  328 HIS
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  123 GLU
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  244 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  328 HIS
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  123 GLU
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  173 ILE
Chi-restraints excluded: chain C residue  176 LEU
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  244 ILE
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain C residue  328 HIS
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  123 GLU
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  173 ILE
Chi-restraints excluded: chain D residue  176 LEU
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  244 ILE
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  320 VAL
Chi-restraints excluded: chain D residue  328 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 61 optimal weight:    0.1980
   chunk 73 optimal weight:    0.7980
   chunk 76 optimal weight:    9.9990
   chunk 87 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 88 optimal weight:    0.0970
   chunk 92 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.4978

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.201801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.134582 restraints weight = 10804.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 2.03
r_work: 0.3439 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.4368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8504  Z= 0.147
  Angle     :  0.480   6.597  11508  Z= 0.251
  Chirality :  0.035   0.145   1252
  Planarity :  0.003   0.024   1392
  Dihedral  : 10.601 155.054   1140
  Min Nonbonded Distance : 2.654

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 20.71 %
    Favored  : 75.48 %
  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:  2.31 (0.27), residues: 988
  helix:  2.31 (0.18), residues: 828
  sheet:  None (None), residues: 0
  loop : -2.95 (0.37), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 146 
 HIS   0.002   0.001   HIS A 324 
 PHE   0.011   0.001   PHE A 240 
 TYR   0.021   0.001   TYR A  82 
 ARG   0.003   0.000   ARG A 207 

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 0.858 
Fit side-chains
REVERT: A  123 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5249 (pt0)
REVERT: B  123 GLU cc_start: 0.6088 (OUTLIER) cc_final: 0.5149 (pt0)
REVERT: B  162 LYS cc_start: 0.5429 (pttp) cc_final: 0.5210 (pttp)
REVERT: B  328 HIS cc_start: 0.6580 (OUTLIER) cc_final: 0.5357 (t-90)
REVERT: C  123 GLU cc_start: 0.6085 (OUTLIER) cc_final: 0.5142 (pt0)
REVERT: C  162 LYS cc_start: 0.5431 (pttp) cc_final: 0.5214 (pttp)
REVERT: C  328 HIS cc_start: 0.6580 (OUTLIER) cc_final: 0.5356 (t-90)
REVERT: D  123 GLU cc_start: 0.6094 (OUTLIER) cc_final: 0.5149 (pt0)
REVERT: D  162 LYS cc_start: 0.5447 (pttp) cc_final: 0.5228 (pttp)
REVERT: D  328 HIS cc_start: 0.6580 (OUTLIER) cc_final: 0.5349 (t-90)
  outliers start: 32
  outliers final: 19
  residues processed: 145
  average time/residue: 0.2517
  time to fit residues: 47.1391
Evaluate side-chains
  133 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  123 GLU
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  244 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  328 HIS
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  123 GLU
Chi-restraints excluded: chain C residue  176 LEU
Chi-restraints excluded: chain C residue  244 ILE
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain C residue  328 HIS
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  123 GLU
Chi-restraints excluded: chain D residue  176 LEU
Chi-restraints excluded: chain D residue  244 ILE
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  320 VAL
Chi-restraints excluded: chain D residue  328 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 97 optimal weight:    0.0980
   chunk 37 optimal weight:    9.9990
   chunk 11 optimal weight:    0.0870
   chunk 74 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 56 optimal weight:    0.5980
   chunk 82 optimal weight:    7.9990
   chunk 35 optimal weight:    8.9990
   chunk 34 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9980
   overall best weight:    0.5558

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.201852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.134434 restraints weight = 10713.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 2.01
r_work: 0.3438 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.3318 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.4501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8504  Z= 0.157
  Angle     :  0.517   6.778  11508  Z= 0.264
  Chirality :  0.036   0.126   1252
  Planarity :  0.003   0.023   1392
  Dihedral  : 10.596 155.299   1140
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 20.95 %
    Favored  : 74.88 %
  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:  2.39 (0.27), residues: 988
  helix:  2.37 (0.18), residues: 828
  sheet:  None (None), residues: 0
  loop : -2.95 (0.37), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 146 
 HIS   0.002   0.001   HIS A 324 
 PHE   0.011   0.001   PHE A 240 
 TYR   0.020   0.001   TYR A  82 
 ARG   0.003   0.000   ARG A 207 

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 104
  time to evaluate  : 0.858 
Fit side-chains
REVERT: A   87 ARG cc_start: 0.6850 (tpp80) cc_final: 0.6604 (tpt170)
REVERT: A  123 GLU cc_start: 0.6086 (OUTLIER) cc_final: 0.5203 (pt0)
REVERT: B   87 ARG cc_start: 0.6802 (tpp80) cc_final: 0.6596 (tpt170)
REVERT: B  123 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5226 (pt0)
REVERT: B  162 LYS cc_start: 0.5453 (pttp) cc_final: 0.5228 (pttp)
REVERT: B  328 HIS cc_start: 0.6602 (OUTLIER) cc_final: 0.5359 (t-90)
REVERT: C  123 GLU cc_start: 0.6123 (OUTLIER) cc_final: 0.5212 (pt0)
REVERT: C  162 LYS cc_start: 0.5453 (pttp) cc_final: 0.5227 (pttp)
REVERT: C  328 HIS cc_start: 0.6599 (OUTLIER) cc_final: 0.5362 (t-90)
REVERT: D  123 GLU cc_start: 0.6141 (OUTLIER) cc_final: 0.5225 (pt0)
REVERT: D  162 LYS cc_start: 0.5472 (pttp) cc_final: 0.5245 (pttp)
REVERT: D  328 HIS cc_start: 0.6599 (OUTLIER) cc_final: 0.5350 (t-90)
  outliers start: 35
  outliers final: 26
  residues processed: 139
  average time/residue: 0.2550
  time to fit residues: 45.8769
Evaluate side-chains
  135 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 102
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  123 GLU
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  244 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  328 HIS
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  123 GLU
Chi-restraints excluded: chain C residue  173 ILE
Chi-restraints excluded: chain C residue  176 LEU
Chi-restraints excluded: chain C residue  244 ILE
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain C residue  328 HIS
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  123 GLU
Chi-restraints excluded: chain D residue  173 ILE
Chi-restraints excluded: chain D residue  176 LEU
Chi-restraints excluded: chain D residue  244 ILE
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  320 VAL
Chi-restraints excluded: chain D residue  328 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 54 optimal weight:    7.9990
   chunk 56 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 63 optimal weight:    0.8980
   chunk 93 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 27 optimal weight:    7.9990
   chunk 67 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.200899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.133044 restraints weight = 10674.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 1.98
r_work: 0.3419 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.4524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8504  Z= 0.180
  Angle     :  0.534   7.108  11508  Z= 0.276
  Chirality :  0.037   0.137   1252
  Planarity :  0.003   0.024   1392
  Dihedral  : 10.623 155.227   1140
  Min Nonbonded Distance : 2.653

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 20.60 %
    Favored  : 74.88 %
  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:  2.35 (0.27), residues: 988
  helix:  2.35 (0.18), residues: 828
  sheet:  None (None), residues: 0
  loop : -3.02 (0.36), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 146 
 HIS   0.002   0.001   HIS A 324 
 PHE   0.011   0.001   PHE D 137 
 TYR   0.019   0.001   TYR A  82 
 ARG   0.003   0.000   ARG D 207 

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 111
  time to evaluate  : 0.881 
Fit side-chains
REVERT: A  123 GLU cc_start: 0.6100 (OUTLIER) cc_final: 0.5205 (pt0)
REVERT: B   87 ARG cc_start: 0.6895 (tpp80) cc_final: 0.6641 (tpt170)
REVERT: B  123 GLU cc_start: 0.6164 (OUTLIER) cc_final: 0.5242 (pt0)
REVERT: B  328 HIS cc_start: 0.6614 (OUTLIER) cc_final: 0.5354 (t-90)
REVERT: C  123 GLU cc_start: 0.6162 (OUTLIER) cc_final: 0.5239 (pt0)
REVERT: C  328 HIS cc_start: 0.6613 (OUTLIER) cc_final: 0.5373 (t-90)
REVERT: D  123 GLU cc_start: 0.6169 (OUTLIER) cc_final: 0.5244 (pt0)
REVERT: D  328 HIS cc_start: 0.6605 (OUTLIER) cc_final: 0.5352 (t-90)
  outliers start: 38
  outliers final: 23
  residues processed: 145
  average time/residue: 0.2760
  time to fit residues: 52.6316
Evaluate side-chains
  141 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 111
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  123 GLU
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  244 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  328 HIS
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  123 GLU
Chi-restraints excluded: chain C residue  173 ILE
Chi-restraints excluded: chain C residue  244 ILE
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain C residue  328 HIS
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  123 GLU
Chi-restraints excluded: chain D residue  173 ILE
Chi-restraints excluded: chain D residue  244 ILE
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  320 VAL
Chi-restraints excluded: chain D residue  328 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 37 optimal weight:    9.9990
   chunk 86 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0980
   chunk 43 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.6188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.197884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.129650 restraints weight = 10653.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 1.95
r_work: 0.3365 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.4342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   8504  Z= 0.261
  Angle     :  0.622  12.472  11508  Z= 0.310
  Chirality :  0.041   0.162   1252
  Planarity :  0.003   0.029   1392
  Dihedral  : 10.737 154.077   1140
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 20.83 %
    Favored  : 75.00 %
  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:  2.11 (0.27), residues: 988
  helix:  2.18 (0.18), residues: 828
  sheet:  None (None), residues: 0
  loop : -3.08 (0.38), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 146 
 HIS   0.002   0.001   HIS A 324 
 PHE   0.017   0.002   PHE A 137 
 TYR   0.019   0.002   TYR A  82 
 ARG   0.004   0.001   ARG B 160 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5975.41 seconds
wall clock time: 103 minutes 37.87 seconds (6217.87 seconds total)