Starting phenix.real_space_refine
on Tue Mar 11 15:09:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sau_24957/03_2025/7sau_24957.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sau_24957/03_2025/7sau_24957.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sau_24957/03_2025/7sau_24957.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sau_24957/03_2025/7sau_24957.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sau_24957/03_2025/7sau_24957.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sau_24957/03_2025/7sau_24957.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    4140      2.51       5
     N    1018      2.21       5
     O    1135      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 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: 6317
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1749
          Classifications: {'peptide': 219}
          Link IDs: {'PTRANS': 5, 'TRANS': 213}
    Chain: "B"
      Number of atoms: 1731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1731
          Classifications: {'peptide': 216}
          Link IDs: {'PTRANS': 5, 'TRANS': 210}
    Chain: "C"
      Number of atoms: 564
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 564
          Classifications: {'peptide': 71}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 67}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 567
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 3, 'TRANS': 67}
    Chain: "E"
      Number of atoms: 572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 572
          Classifications: {'peptide': 72}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 68}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 567
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 3, 'TRANS': 67}
    Chain: "G"
      Number of atoms: 567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 567
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 3, 'TRANS': 67}
  Time building chain proxies: 4.20, per 1000 atoms: 0.66
  Number of scatterers: 6317
  At special positions: 0
  Unit cell: (70.72, 69.056, 134.784, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      24     16.00
     O    1135      8.00
     N    1018      7.00
     C    4140      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: 1.62
  Conformation dependent library (CDL) restraints added in 924.6 milliseconds
  

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1484

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 1 sheets defined
      76.4% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 23
    Processing helix  chain 'A' and resid 24 through 26
      No H-bonds generated for 'chain 'A' and resid 24 through 26'
    Processing helix  chain 'A' and resid 29 through 68
      removed outlier: 3.795A  pdb=" N   PHE A  56 " --> pdb=" O   LYS A  52 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ILE A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLU A  67 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ASN A  68 " --> pdb=" O   ALA A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 104
    Processing helix  chain 'A' and resid 122 through 127
    Processing helix  chain 'A' and resid 134 through 150
    Processing helix  chain 'A' and resid 151 through 153
      No H-bonds generated for 'chain 'A' and resid 151 through 153'
    Processing helix  chain 'A' and resid 156 through 167
    Processing helix  chain 'A' and resid 180 through 187
    Processing helix  chain 'A' and resid 190 through 219
      Proline residue:  A 196  - end of helix
      removed outlier: 3.697A  pdb=" N   ASN A 219 " --> pdb=" O   HIS A 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 28
      removed outlier: 4.738A  pdb=" N   LEU B  18 " --> pdb=" O   ASN B  14 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   VAL B  19 " --> pdb=" O   MET B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 66
      removed outlier: 3.781A  pdb=" N   PHE B  56 " --> pdb=" O   LYS B  52 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ILE B  57 " --> pdb=" O   LYS B  53 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   TYR B  58 " --> pdb=" O   LEU B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 103
      removed outlier: 3.567A  pdb=" N   ALA B  72 " --> pdb=" O   ASN B  68 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   VAL B  74 " --> pdb=" O   GLU B  70 " (cutoff:3.500A)
      removed outlier: 4.821A  pdb=" N   TRP B  75 " --> pdb=" O   LYS B  71 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   VAL B  82 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 129
    Processing helix  chain 'B' and resid 130 through 132
      No H-bonds generated for 'chain 'B' and resid 130 through 132'
    Processing helix  chain 'B' and resid 133 through 152
      removed outlier: 4.309A  pdb=" N   GLU B 137 " --> pdb=" O   GLY B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 167
    Processing helix  chain 'B' and resid 182 through 187
      removed outlier: 3.537A  pdb=" N   PHE B 186 " --> pdb=" O   GLU B 182 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLU B 187 " --> pdb=" O   ASN B 183 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 182 through 187'
    Processing helix  chain 'B' and resid 190 through 218
      Proline residue:  B 196  - end of helix
      removed outlier: 3.689A  pdb=" N   HIS B 215 " --> pdb=" O   ASP B 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 9 through 36
    Processing helix  chain 'C' and resid 39 through 59
    Processing helix  chain 'C' and resid 68 through 72
    Processing helix  chain 'D' and resid 9 through 36
    Processing helix  chain 'D' and resid 39 through 58
      removed outlier: 3.623A  pdb=" N   ILE D  45 " --> pdb=" O   ASP D  41 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 59 through 61
      No H-bonds generated for 'chain 'D' and resid 59 through 61'
    Processing helix  chain 'D' and resid 68 through 72
    Processing helix  chain 'E' and resid 8 through 36
      removed outlier: 3.614A  pdb=" N   LYS E  12 " --> pdb=" O   GLY E   8 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   PHE E  14 " --> pdb=" O   LYS E  10 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   LYS E  17 " --> pdb=" O   ASN E  13 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 39 through 58
    Processing helix  chain 'E' and resid 68 through 72
    Processing helix  chain 'F' and resid 9 through 36
      removed outlier: 3.517A  pdb=" N   PHE F  14 " --> pdb=" O   LYS F  10 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   TYR F  19 " --> pdb=" O   LEU F  15 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 39 through 59
      removed outlier: 3.532A  pdb=" N   MET F  43 " --> pdb=" O   GLY F  39 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA F  59 " --> pdb=" O   PHE F  55 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 9 through 36
      removed outlier: 3.503A  pdb=" N   PHE G  14 " --> pdb=" O   LYS G  10 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   TYR G  19 " --> pdb=" O   LEU G  15 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 39 through 59
    Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 174
      removed outlier: 3.727A  pdb=" N   VAL A 177 " --> pdb=" O   VAL A 174 " (cutoff:3.500A)

    448 hydrogen bonds defined for protein.
    1323 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: 1.55

  Time building geometry restraints manager: 1.89 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1979
        1.34 -     1.46: 920
        1.46 -     1.57: 3508
        1.57 -     1.69: 0
        1.69 -     1.80: 48
  Bond restraints: 6455
  Sorted by residual:
  bond pdb=" CB  PRO C  74 "
       pdb=" CG  PRO C  74 "
    ideal  model  delta    sigma   weight residual
    1.492  1.569 -0.077 5.00e-02 4.00e+02 2.35e+00
  bond pdb=" CG1 ILE B  28 "
       pdb=" CD1 ILE B  28 "
    ideal  model  delta    sigma   weight residual
    1.513  1.455  0.058 3.90e-02 6.57e+02 2.23e+00
  bond pdb=" CB  VAL A  82 "
       pdb=" CG1 VAL A  82 "
    ideal  model  delta    sigma   weight residual
    1.521  1.473  0.048 3.30e-02 9.18e+02 2.14e+00
  bond pdb=" CB  MET A  16 "
       pdb=" CG  MET A  16 "
    ideal  model  delta    sigma   weight residual
    1.520  1.480  0.040 3.00e-02 1.11e+03 1.81e+00
  bond pdb=" CB  ARG A 139 "
       pdb=" CG  ARG A 139 "
    ideal  model  delta    sigma   weight residual
    1.520  1.482  0.038 3.00e-02 1.11e+03 1.61e+00
  ... (remaining 6450 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 8448
        1.47 -     2.95: 200
        2.95 -     4.42: 57
        4.42 -     5.90: 7
        5.90 -     7.37: 5
  Bond angle restraints: 8717
  Sorted by residual:
  angle pdb=" CA  ARG B 120 "
        pdb=" C   ARG B 120 "
        pdb=" N   GLU B 121 "
      ideal   model   delta    sigma   weight residual
     116.84  122.70   -5.86 1.71e+00 3.42e-01 1.17e+01
  angle pdb=" C   MET B  16 "
        pdb=" N   TYR B  17 "
        pdb=" CA  TYR B  17 "
      ideal   model   delta    sigma   weight residual
     120.31  115.17    5.14 1.52e+00 4.33e-01 1.14e+01
  angle pdb=" N   LEU A 128 "
        pdb=" CA  LEU A 128 "
        pdb=" C   LEU A 128 "
      ideal   model   delta    sigma   weight residual
     110.80  117.77   -6.97 2.13e+00 2.20e-01 1.07e+01
  angle pdb=" CA  ARG B 120 "
        pdb=" C   ARG B 120 "
        pdb=" O   ARG B 120 "
      ideal   model   delta    sigma   weight residual
     120.51  116.47    4.04 1.43e+00 4.89e-01 7.97e+00
  angle pdb=" CB  ARG B  76 "
        pdb=" CG  ARG B  76 "
        pdb=" CD  ARG B  76 "
      ideal   model   delta    sigma   weight residual
     111.30  117.73   -6.43 2.30e+00 1.89e-01 7.82e+00
  ... (remaining 8712 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.04: 3427
       17.04 -    34.07: 343
       34.07 -    51.11: 48
       51.11 -    68.15: 14
       68.15 -    85.19: 5
  Dihedral angle restraints: 3837
    sinusoidal: 1542
      harmonic: 2295
  Sorted by residual:
  dihedral pdb=" CA  GLU A 131 "
           pdb=" C   GLU A 131 "
           pdb=" N   GLY A 132 "
           pdb=" CA  GLY A 132 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.44  -20.56     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  TRP D  37 "
           pdb=" C   TRP D  37 "
           pdb=" N   THR D  38 "
           pdb=" CA  THR D  38 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.42  -18.58     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  TRP F  37 "
           pdb=" C   TRP F  37 "
           pdb=" N   THR F  38 "
           pdb=" CA  THR F  38 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.52  -18.48     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 3834 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 539
       0.029 -    0.058: 304
       0.058 -    0.086: 89
       0.086 -    0.115: 37
       0.115 -    0.144: 5
  Chirality restraints: 974
  Sorted by residual:
  chirality pdb=" CA  ASP A 211 "
            pdb=" N   ASP A 211 "
            pdb=" C   ASP A 211 "
            pdb=" CB  ASP A 211 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.19e-01
  chirality pdb=" CA  GLN B 151 "
            pdb=" N   GLN B 151 "
            pdb=" C   GLN B 151 "
            pdb=" CB  GLN B 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.75e-01
  chirality pdb=" CA  PRO A 196 "
            pdb=" N   PRO A 196 "
            pdb=" C   PRO A 196 "
            pdb=" CB  PRO A 196 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.51e-01
  ... (remaining 971 not shown)

  Planarity restraints: 1095
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR G  73 "    0.073 5.00e-02 4.00e+02   1.10e-01 1.93e+01
        pdb=" N   PRO G  74 "   -0.190 5.00e-02 4.00e+02
        pdb=" CA  PRO G  74 "    0.059 5.00e-02 4.00e+02
        pdb=" CD  PRO G  74 "    0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C  73 "    0.055 5.00e-02 4.00e+02   8.19e-02 1.07e+01
        pdb=" N   PRO C  74 "   -0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO C  74 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO C  74 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR E  73 "   -0.029 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO E  74 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO E  74 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO E  74 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1092 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 66
        2.68 -     3.23: 6309
        3.23 -     3.79: 9837
        3.79 -     4.34: 13280
        4.34 -     4.90: 21807
  Nonbonded interactions: 51299
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  58 "
            pdb=" OE2 GLU B 209 "
     model   vdw
     2.122 3.040
  nonbonded pdb=" OD2 ASP A  62 "
            pdb=" OH  TYR A  80 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OH  TYR A  58 "
            pdb=" OE2 GLU A 209 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   ASN B 119 "
            pdb=" ND2 ASN B 119 "
     model   vdw
     2.314 3.120
  nonbonded pdb=" OD1 ASN B 125 "
            pdb=" N   TYR B 126 "
     model   vdw
     2.359 3.120
  ... (remaining 51294 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 5 through 220)
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'D' and (resid 6 through 75 or (resid 76 and (name N or name CA or name C \ 
 or name O or name CB ))))
  selection = (chain 'E' and resid 6 through 76)
  selection = (chain 'F' and (resid 6 through 75 or (resid 76 and (name N or name CA or name C \ 
 or name O or name CB ))))
  selection = (chain 'G' and (resid 6 through 75 or (resid 76 and (name N or name CA or name C \ 
 or name O or name CB ))))
}

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:             0.660
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     18.060
  Find NCS groups from input model:        0.220
  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:11.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
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      :  0.005   0.077   6455  Z= 0.309
  Angle     :  0.606   7.370   8717  Z= 0.331
  Chirality :  0.040   0.144    974
  Planarity :  0.005   0.110   1095
  Dihedral  : 13.767  85.186   2353
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.00 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.30), residues: 777
  helix:  0.82 (0.21), residues: 573
  sheet:  None (None), residues: 0
  loop : -0.46 (0.48), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  75 
 HIS   0.003   0.001   HIS A 188 
 PHE   0.012   0.001   PHE G  55 
 TYR   0.031   0.002   TYR B  17 
 ARG   0.012   0.001   ARG B  76 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 156
  time to evaluate  : 0.689 
Fit side-chains
REVERT: A   30 LYS cc_start: 0.7710 (tmmt) cc_final: 0.7429 (ttmm)
REVERT: A   38 LYS cc_start: 0.7866 (mmmt) cc_final: 0.7155 (mmtp)
REVERT: A   59 GLN cc_start: 0.7322 (mt0) cc_final: 0.6849 (mp10)
REVERT: A   84 LYS cc_start: 0.7920 (tttp) cc_final: 0.7515 (ttmp)
REVERT: A  118 ASP cc_start: 0.8119 (p0) cc_final: 0.7882 (p0)
REVERT: B   34 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6805 (mm-30)
REVERT: B   80 TYR cc_start: 0.6974 (m-80) cc_final: 0.6663 (m-10)
REVERT: B   85 GLN cc_start: 0.7652 (mt0) cc_final: 0.7330 (mt0)
REVERT: B   91 ASN cc_start: 0.7662 (m-40) cc_final: 0.7424 (m-40)
REVERT: B  113 ARG cc_start: 0.7124 (mtt180) cc_final: 0.6588 (mtt90)
REVERT: B  122 LYS cc_start: 0.7702 (mttp) cc_final: 0.7426 (mtmt)
REVERT: B  126 TYR cc_start: 0.8093 (t80) cc_final: 0.7632 (t80)
REVERT: B  143 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6410 (mt-10)
REVERT: B  149 MET cc_start: 0.7400 (mmp) cc_final: 0.7137 (mpm)
REVERT: C   33 LYS cc_start: 0.8531 (tptm) cc_final: 0.8317 (tptp)
REVERT: D   38 THR cc_start: 0.8002 (p) cc_final: 0.7799 (m)
REVERT: D   43 MET cc_start: 0.8181 (mtp) cc_final: 0.7948 (mtp)
REVERT: E   33 LYS cc_start: 0.8641 (tptt) cc_final: 0.8297 (tppt)
REVERT: E   41 ASP cc_start: 0.7976 (m-30) cc_final: 0.7751 (m-30)
REVERT: F   13 ASN cc_start: 0.7162 (t0) cc_final: 0.6864 (m110)
REVERT: F   61 GLU cc_start: 0.7110 (pt0) cc_final: 0.6891 (pt0)
REVERT: G    7 ASN cc_start: 0.6154 (m110) cc_final: 0.5764 (m-40)
REVERT: G   62 LYS cc_start: 0.5998 (mppt) cc_final: 0.5785 (mttp)
REVERT: G   67 TYR cc_start: 0.7524 (m-80) cc_final: 0.7272 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 156
  average time/residue: 1.2771
  time to fit residues: 207.9651
Evaluate side-chains
  115 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 31 optimal weight:    9.9990
   chunk 60 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    8.9990
   chunk 44 optimal weight:    0.7980
   chunk 69 optimal weight:    0.0010
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
A 148 ASN
B  40 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.139765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.099155 restraints weight = 7326.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 1.77
r_work: 0.2859 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2717 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.1482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6455  Z= 0.187
  Angle     :  0.534   7.377   8717  Z= 0.283
  Chirality :  0.038   0.143    974
  Planarity :  0.005   0.077   1095
  Dihedral  :  4.153  19.887    833
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  :  9.24 %
    Favored  : 88.79 %
  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:  1.62 (0.30), residues: 777
  helix:  1.62 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop : -0.44 (0.48), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.000   TRP A  75 
 HIS   0.002   0.001   HIS E  36 
 PHE   0.015   0.001   PHE E  55 
 TYR   0.015   0.001   TYR A  80 
 ARG   0.007   0.001   ARG B  76 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 0.674 
Fit side-chains
REVERT: A   30 LYS cc_start: 0.7391 (tmmt) cc_final: 0.7062 (ttmm)
REVERT: A   38 LYS cc_start: 0.8149 (mmmt) cc_final: 0.7223 (mmtp)
REVERT: A   59 GLN cc_start: 0.7632 (mt0) cc_final: 0.6961 (mp10)
REVERT: A   84 LYS cc_start: 0.8020 (tttp) cc_final: 0.7612 (ttmp)
REVERT: A   88 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7850 (mm-30)
REVERT: A  118 ASP cc_start: 0.8478 (p0) cc_final: 0.8207 (p0)
REVERT: A  211 ASP cc_start: 0.7834 (p0) cc_final: 0.7603 (p0)
REVERT: A  214 SER cc_start: 0.8126 (m) cc_final: 0.7660 (p)
REVERT: A  217 GLN cc_start: 0.8007 (tt0) cc_final: 0.7127 (pt0)
REVERT: B   34 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7188 (mm-30)
REVERT: B   76 ARG cc_start: 0.6335 (ttp-110) cc_final: 0.6127 (ttp-110)
REVERT: B   80 TYR cc_start: 0.7046 (m-80) cc_final: 0.6697 (m-10)
REVERT: B   91 ASN cc_start: 0.7695 (m-40) cc_final: 0.7474 (m-40)
REVERT: B  113 ARG cc_start: 0.7071 (mtt180) cc_final: 0.6461 (mtt90)
REVERT: B  126 TYR cc_start: 0.8038 (t80) cc_final: 0.7508 (t80)
REVERT: B  131 GLU cc_start: 0.7054 (mp0) cc_final: 0.6768 (mp0)
REVERT: B  143 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6721 (mt-10)
REVERT: B  149 MET cc_start: 0.7427 (mmp) cc_final: 0.7053 (mpm)
REVERT: B  163 LEU cc_start: 0.7041 (mt) cc_final: 0.6740 (mp)
REVERT: B  182 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7976 (pm20)
REVERT: C   33 LYS cc_start: 0.8540 (tptm) cc_final: 0.8306 (tptp)
REVERT: E   10 LYS cc_start: 0.7471 (mtmt) cc_final: 0.7015 (mttm)
REVERT: E   25 ILE cc_start: 0.8657 (mm) cc_final: 0.8350 (mt)
REVERT: E   33 LYS cc_start: 0.8727 (tptt) cc_final: 0.8472 (tppt)
REVERT: F   61 GLU cc_start: 0.7499 (pt0) cc_final: 0.7202 (pt0)
REVERT: G    7 ASN cc_start: 0.6050 (m110) cc_final: 0.5622 (m-40)
REVERT: G   41 ASP cc_start: 0.7769 (m-30) cc_final: 0.7472 (m-30)
REVERT: G   62 LYS cc_start: 0.6482 (mppt) cc_final: 0.6057 (mttp)
REVERT: G   67 TYR cc_start: 0.7570 (m-80) cc_final: 0.7234 (m-80)
  outliers start: 13
  outliers final: 3
  residues processed: 133
  average time/residue: 1.3253
  time to fit residues: 183.8862
Evaluate side-chains
  114 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 110
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  182 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 62 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9980
   chunk 7 optimal weight:    6.9990
   chunk 15 optimal weight:    0.0670
   chunk 24 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.7718

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

Flipped N/Q/H residues before XYZ refinement:
A  90 HIS
A 219 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.141298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.100694 restraints weight = 7432.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 1.79
r_work: 0.2902 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2760 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6455  Z= 0.174
  Angle     :  0.509   7.327   8717  Z= 0.266
  Chirality :  0.037   0.130    974
  Planarity :  0.004   0.064   1095
  Dihedral  :  4.034  19.527    833
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 13.48 %
    Favored  : 83.94 %
  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:  2.05 (0.31), residues: 777
  helix:  2.05 (0.21), residues: 563
  sheet:  None (None), residues: 0
  loop : -0.50 (0.46), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E  69 
 HIS   0.002   0.001   HIS E  36 
 PHE   0.012   0.001   PHE G  55 
 TYR   0.013   0.001   TYR A  80 
 ARG   0.010   0.001   ARG A 218 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.700 
Fit side-chains
REVERT: A   30 LYS cc_start: 0.7484 (tmmt) cc_final: 0.7033 (ttmm)
REVERT: A   34 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7570 (mm-30)
REVERT: A   38 LYS cc_start: 0.8182 (mmmt) cc_final: 0.7257 (mmtp)
REVERT: A   84 LYS cc_start: 0.8023 (tttp) cc_final: 0.7577 (ttmp)
REVERT: A   88 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7867 (mm-30)
REVERT: A  118 ASP cc_start: 0.8415 (p0) cc_final: 0.8083 (p0)
REVERT: A  164 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7539 (pt0)
REVERT: A  214 SER cc_start: 0.7965 (m) cc_final: 0.7538 (p)
REVERT: A  217 GLN cc_start: 0.8061 (tt0) cc_final: 0.7179 (pt0)
REVERT: B   34 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7268 (mm-30)
REVERT: B   80 TYR cc_start: 0.7103 (m-80) cc_final: 0.6698 (m-10)
REVERT: B  113 ARG cc_start: 0.7155 (mtt180) cc_final: 0.6526 (mtt90)
REVERT: B  126 TYR cc_start: 0.8009 (t80) cc_final: 0.7571 (t80)
REVERT: B  131 GLU cc_start: 0.7069 (mp0) cc_final: 0.6817 (mp0)
REVERT: B  143 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6571 (mt-10)
REVERT: B  162 MET cc_start: 0.7185 (tmm) cc_final: 0.6974 (tmm)
REVERT: D   43 MET cc_start: 0.8569 (mtp) cc_final: 0.8357 (mtp)
REVERT: E   25 ILE cc_start: 0.8738 (mm) cc_final: 0.8452 (mt)
REVERT: E   33 LYS cc_start: 0.8732 (tptt) cc_final: 0.8479 (tppt)
REVERT: F   61 GLU cc_start: 0.7528 (pt0) cc_final: 0.7229 (pt0)
REVERT: G    7 ASN cc_start: 0.6062 (m110) cc_final: 0.5625 (m-40)
REVERT: G   41 ASP cc_start: 0.7705 (m-30) cc_final: 0.7421 (m-30)
REVERT: G   62 LYS cc_start: 0.6530 (mppt) cc_final: 0.6128 (mttp)
REVERT: G   67 TYR cc_start: 0.7602 (m-80) cc_final: 0.7287 (m-80)
  outliers start: 17
  outliers final: 5
  residues processed: 126
  average time/residue: 1.3310
  time to fit residues: 175.7166
Evaluate side-chains
  113 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 108
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain D residue   58 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 37 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 32 optimal weight:    9.9990
   chunk 76 optimal weight:    0.1980
   chunk 46 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 219 ASN
B  85 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.140481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.100010 restraints weight = 7513.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 1.83
r_work: 0.2893 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2747 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6455  Z= 0.188
  Angle     :  0.513   7.831   8717  Z= 0.267
  Chirality :  0.038   0.143    974
  Planarity :  0.004   0.055   1095
  Dihedral  :  3.995  19.309    833
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.39 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.18 (0.31), residues: 777
  helix:  2.16 (0.21), residues: 565
  sheet:  None (None), residues: 0
  loop : -0.52 (0.46), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  69 
 HIS   0.002   0.001   HIS E  36 
 PHE   0.015   0.001   PHE G  55 
 TYR   0.015   0.001   TYR A  80 
 ARG   0.012   0.001   ARG A 218 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.747 
Fit side-chains
REVERT: A   30 LYS cc_start: 0.7651 (tmmt) cc_final: 0.7140 (ttmm)
REVERT: A   34 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7599 (mm-30)
REVERT: A   38 LYS cc_start: 0.8214 (mmmt) cc_final: 0.7372 (mmtp)
REVERT: A   59 GLN cc_start: 0.7719 (mt0) cc_final: 0.7114 (mp-120)
REVERT: A   84 LYS cc_start: 0.8070 (tttp) cc_final: 0.7634 (ttmp)
REVERT: A   88 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7886 (mm-30)
REVERT: A  118 ASP cc_start: 0.8438 (p0) cc_final: 0.8114 (p0)
REVERT: A  214 SER cc_start: 0.8074 (m) cc_final: 0.7661 (p)
REVERT: A  217 GLN cc_start: 0.8111 (tt0) cc_final: 0.7243 (pt0)
REVERT: B   34 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7418 (mm-30)
REVERT: B   80 TYR cc_start: 0.7119 (m-80) cc_final: 0.6717 (m-10)
REVERT: B  113 ARG cc_start: 0.7110 (mtt180) cc_final: 0.6629 (mtt90)
REVERT: B  126 TYR cc_start: 0.8085 (t80) cc_final: 0.7634 (t80)
REVERT: B  139 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7148 (ttm-80)
REVERT: B  143 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6696 (mt-10)
REVERT: E   10 LYS cc_start: 0.7287 (mtpp) cc_final: 0.6793 (mtmm)
REVERT: E   25 ILE cc_start: 0.8803 (mm) cc_final: 0.8540 (mt)
REVERT: E   33 LYS cc_start: 0.8768 (tptt) cc_final: 0.8546 (tppt)
REVERT: F   61 GLU cc_start: 0.7450 (pt0) cc_final: 0.7144 (pt0)
REVERT: G   41 ASP cc_start: 0.7703 (m-30) cc_final: 0.7416 (m-30)
REVERT: G   62 LYS cc_start: 0.6450 (mppt) cc_final: 0.6007 (mttp)
REVERT: G   67 TYR cc_start: 0.7651 (m-80) cc_final: 0.7306 (m-80)
  outliers start: 16
  outliers final: 8
  residues processed: 118
  average time/residue: 1.2975
  time to fit residues: 160.1464
Evaluate side-chains
  117 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  136 ARG
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain D residue   58 SER
Chi-restraints excluded: chain F residue   15 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 42 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 219 ASN
B 148 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.139418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.098858 restraints weight = 7386.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3046 rms_B_bonded: 1.83
r_work: 0.2899 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2753 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6455  Z= 0.183
  Angle     :  0.504   8.007   8717  Z= 0.263
  Chirality :  0.038   0.139    974
  Planarity :  0.004   0.050   1095
  Dihedral  :  3.967  19.276    833
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 14.70 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.29 (0.30), residues: 777
  helix:  2.24 (0.21), residues: 565
  sheet:  None (None), residues: 0
  loop : -0.49 (0.46), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  69 
 HIS   0.002   0.001   HIS A 188 
 PHE   0.014   0.001   PHE G  55 
 TYR   0.014   0.001   TYR A  80 
 ARG   0.012   0.001   ARG A 218 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 0.711 
Fit side-chains
REVERT: A   30 LYS cc_start: 0.7669 (tmmt) cc_final: 0.7159 (ttmm)
REVERT: A   34 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7588 (mm-30)
REVERT: A   38 LYS cc_start: 0.8233 (mmmt) cc_final: 0.7087 (mmtp)
REVERT: A   42 ASP cc_start: 0.8019 (m-30) cc_final: 0.7455 (m-30)
REVERT: A   59 GLN cc_start: 0.7684 (mt0) cc_final: 0.7057 (mp10)
REVERT: A   84 LYS cc_start: 0.8093 (tttp) cc_final: 0.7663 (ttmp)
REVERT: A   87 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8167 (m-30)
REVERT: A  103 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.7878 (tp)
REVERT: A  118 ASP cc_start: 0.8406 (p0) cc_final: 0.8083 (p0)
REVERT: A  162 MET cc_start: 0.8089 (pp-130) cc_final: 0.7811 (ppp)
REVERT: A  164 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7647 (pt0)
REVERT: A  214 SER cc_start: 0.8066 (m) cc_final: 0.7657 (p)
REVERT: A  217 GLN cc_start: 0.8116 (tt0) cc_final: 0.7253 (pt0)
REVERT: B   34 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7410 (mm-30)
REVERT: B   80 TYR cc_start: 0.7174 (m-80) cc_final: 0.6816 (m-10)
REVERT: B   91 ASN cc_start: 0.7801 (m-40) cc_final: 0.7599 (m-40)
REVERT: B  113 ARG cc_start: 0.7145 (mtt180) cc_final: 0.6656 (mtt90)
REVERT: B  126 TYR cc_start: 0.8089 (t80) cc_final: 0.7671 (t80)
REVERT: B  139 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7564 (ttm-80)
REVERT: E   10 LYS cc_start: 0.7300 (mtpp) cc_final: 0.6791 (mtmt)
REVERT: E   25 ILE cc_start: 0.8807 (mm) cc_final: 0.8550 (mt)
REVERT: E   33 LYS cc_start: 0.8785 (tptt) cc_final: 0.8520 (tppt)
REVERT: F   15 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.6964 (mt)
REVERT: G   41 ASP cc_start: 0.7700 (m-30) cc_final: 0.7390 (m-30)
REVERT: G   62 LYS cc_start: 0.6426 (mppt) cc_final: 0.5983 (mttp)
REVERT: G   67 TYR cc_start: 0.7670 (m-80) cc_final: 0.7363 (m-80)
  outliers start: 20
  outliers final: 7
  residues processed: 126
  average time/residue: 1.2031
  time to fit residues: 158.9807
Evaluate side-chains
  118 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue  103 ILE
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  136 ARG
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain D residue   58 SER
Chi-restraints excluded: chain F residue   15 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 56 optimal weight:    0.3980
   chunk 35 optimal weight:    5.9990
   chunk 48 optimal weight:    0.0980
   chunk 12 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 18 optimal weight:    0.2980
   chunk 62 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 219 ASN
G  36 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.142992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.102203 restraints weight = 7281.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 1.77
r_work: 0.2890 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2744 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   6455  Z= 0.147
  Angle     :  0.482   8.394   8717  Z= 0.253
  Chirality :  0.037   0.134    974
  Planarity :  0.004   0.047   1095
  Dihedral  :  3.853  18.738    833
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.52 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.42 (0.31), residues: 777
  helix:  2.36 (0.21), residues: 569
  sheet:  None (None), residues: 0
  loop : -0.58 (0.47), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP B  75 
 HIS   0.002   0.001   HIS C  36 
 PHE   0.013   0.001   PHE E  55 
 TYR   0.013   0.001   TYR A  80 
 ARG   0.011   0.000   ARG A 218 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.668 
Fit side-chains
REVERT: A   30 LYS cc_start: 0.7368 (tmmt) cc_final: 0.6897 (ttmm)
REVERT: A   34 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7424 (mm-30)
REVERT: A   38 LYS cc_start: 0.8091 (mmmt) cc_final: 0.7166 (mmtp)
REVERT: A   63 LEU cc_start: 0.7512 (mp) cc_final: 0.7256 (mt)
REVERT: A   84 LYS cc_start: 0.7892 (tttp) cc_final: 0.7551 (ttmp)
REVERT: A   87 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8117 (m-30)
REVERT: A  103 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7679 (tp)
REVERT: A  162 MET cc_start: 0.8057 (pp-130) cc_final: 0.7754 (ppp)
REVERT: A  214 SER cc_start: 0.7958 (m) cc_final: 0.7526 (p)
REVERT: A  217 GLN cc_start: 0.8046 (tt0) cc_final: 0.7149 (pt0)
REVERT: B   34 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7113 (mm-30)
REVERT: B   80 TYR cc_start: 0.7117 (m-80) cc_final: 0.6786 (m-10)
REVERT: B  113 ARG cc_start: 0.7078 (mtt180) cc_final: 0.6562 (mtt90)
REVERT: B  126 TYR cc_start: 0.7910 (t80) cc_final: 0.7466 (t80)
REVERT: B  131 GLU cc_start: 0.7128 (mp0) cc_final: 0.6848 (mp0)
REVERT: B  139 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7440 (ttm-80)
REVERT: E   25 ILE cc_start: 0.8764 (mm) cc_final: 0.8489 (mt)
REVERT: E   33 LYS cc_start: 0.8673 (tptt) cc_final: 0.8376 (tppt)
REVERT: F   15 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6784 (mt)
REVERT: G   41 ASP cc_start: 0.7693 (m-30) cc_final: 0.7380 (m-30)
REVERT: G   62 LYS cc_start: 0.6361 (mppt) cc_final: 0.5899 (mttp)
REVERT: G   67 TYR cc_start: 0.7600 (m-80) cc_final: 0.7325 (m-80)
  outliers start: 19
  outliers final: 5
  residues processed: 123
  average time/residue: 1.2950
  time to fit residues: 167.2107
Evaluate side-chains
  119 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue  103 ILE
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain D residue   58 SER
Chi-restraints excluded: chain F residue   15 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 34 optimal weight:    7.9990
   chunk 74 optimal weight:    0.9990
   chunk 47 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0470
   overall best weight:    1.0084

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

Flipped N/Q/H residues before XYZ refinement:
A 219 ASN
G  36 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.140613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.099269 restraints weight = 7315.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 1.80
r_work: 0.2884 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2738 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6455  Z= 0.190
  Angle     :  0.512   8.613   8717  Z= 0.266
  Chirality :  0.038   0.135    974
  Planarity :  0.004   0.049   1095
  Dihedral  :  3.927  19.388    833
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.97 %
    Favored  : 80.15 %
  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 (0.31), residues: 777
  helix:  2.30 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop : -0.51 (0.47), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  75 
 HIS   0.003   0.001   HIS G  36 
 PHE   0.020   0.001   PHE E  55 
 TYR   0.013   0.001   TYR A  80 
 ARG   0.012   0.001   ARG A 218 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.669 
Fit side-chains
REVERT: A   30 LYS cc_start: 0.7430 (tmmt) cc_final: 0.6881 (ttmm)
REVERT: A   34 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7483 (mm-30)
REVERT: A   38 LYS cc_start: 0.8117 (mmmt) cc_final: 0.7201 (mmtp)
REVERT: A   48 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8353 (mtt)
REVERT: A   63 LEU cc_start: 0.7531 (mp) cc_final: 0.7288 (mt)
REVERT: A   84 LYS cc_start: 0.7926 (tttp) cc_final: 0.7654 (ttmp)
REVERT: A   87 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8170 (m-30)
REVERT: A  214 SER cc_start: 0.8043 (m) cc_final: 0.7611 (p)
REVERT: A  217 GLN cc_start: 0.8068 (tt0) cc_final: 0.7173 (pt0)
REVERT: B   34 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7228 (mm-30)
REVERT: B   80 TYR cc_start: 0.7061 (m-80) cc_final: 0.6813 (m-80)
REVERT: B  113 ARG cc_start: 0.7081 (mtt180) cc_final: 0.6556 (mtt90)
REVERT: B  126 TYR cc_start: 0.7913 (t80) cc_final: 0.7529 (t80)
REVERT: B  131 GLU cc_start: 0.7147 (mp0) cc_final: 0.6797 (mp0)
REVERT: B  139 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7492 (ttm-80)
REVERT: C   33 LYS cc_start: 0.8556 (tptp) cc_final: 0.8353 (tppp)
REVERT: E   10 LYS cc_start: 0.7336 (mtpp) cc_final: 0.6790 (mtmt)
REVERT: E   25 ILE cc_start: 0.8828 (mm) cc_final: 0.8545 (mt)
REVERT: E   33 LYS cc_start: 0.8724 (tptt) cc_final: 0.8442 (tppt)
REVERT: F   15 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6734 (mt)
REVERT: G   41 ASP cc_start: 0.7721 (m-30) cc_final: 0.7385 (m-30)
REVERT: G   62 LYS cc_start: 0.6351 (mppt) cc_final: 0.5903 (mttp)
REVERT: G   67 TYR cc_start: 0.7593 (m-80) cc_final: 0.7336 (m-80)
  outliers start: 19
  outliers final: 6
  residues processed: 121
  average time/residue: 1.3218
  time to fit residues: 167.1529
Evaluate side-chains
  116 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 MET
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  136 ARG
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain D residue   58 SER
Chi-restraints excluded: chain F residue   15 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0470
   chunk 37 optimal weight:    7.9990
   chunk 69 optimal weight:    7.9990
   chunk 76 optimal weight:    6.9990
   chunk 44 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 32 optimal weight:    8.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.6278

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

Flipped N/Q/H residues before XYZ refinement:
A 219 ASN
G  36 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.142727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.101980 restraints weight = 7339.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 1.76
r_work: 0.2940 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2797 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.2550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052   6455  Z= 0.158
  Angle     :  0.496   8.886   8717  Z= 0.258
  Chirality :  0.037   0.133    974
  Planarity :  0.004   0.055   1095
  Dihedral  :  3.851  18.958    833
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 18.18 %
    Favored  : 79.55 %
  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:  2.47 (0.31), residues: 777
  helix:  2.41 (0.21), residues: 570
  sheet:  None (None), residues: 0
  loop : -0.61 (0.47), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP B  75 
 HIS   0.002   0.001   HIS G  36 
 PHE   0.018   0.001   PHE E  55 
 TYR   0.013   0.001   TYR A  80 
 ARG   0.015   0.001   ARG A 218 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.798 
Fit side-chains
REVERT: A   30 LYS cc_start: 0.7436 (tmmt) cc_final: 0.6923 (ttmm)
REVERT: A   34 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7452 (mm-30)
REVERT: A   38 LYS cc_start: 0.8145 (mmmt) cc_final: 0.7271 (mmtp)
REVERT: A   48 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8341 (mtt)
REVERT: A   63 LEU cc_start: 0.7568 (mp) cc_final: 0.7318 (mt)
REVERT: A   84 LYS cc_start: 0.7854 (tttp) cc_final: 0.7537 (ttmp)
REVERT: A   87 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8255 (m-30)
REVERT: A  162 MET cc_start: 0.8065 (pp-130) cc_final: 0.7783 (ppp)
REVERT: A  164 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7303 (pt0)
REVERT: A  214 SER cc_start: 0.8004 (m) cc_final: 0.7574 (p)
REVERT: A  217 GLN cc_start: 0.8073 (tt0) cc_final: 0.7200 (pt0)
REVERT: B   34 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7237 (mm-30)
REVERT: B  113 ARG cc_start: 0.7103 (mtt180) cc_final: 0.6581 (mtt90)
REVERT: B  126 TYR cc_start: 0.7934 (t80) cc_final: 0.7490 (t80)
REVERT: B  131 GLU cc_start: 0.7148 (mp0) cc_final: 0.6800 (mp0)
REVERT: B  139 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7505 (ttm-80)
REVERT: E   10 LYS cc_start: 0.7276 (mtpp) cc_final: 0.6800 (mtmt)
REVERT: E   25 ILE cc_start: 0.8825 (mm) cc_final: 0.8547 (mt)
REVERT: E   33 LYS cc_start: 0.8736 (tptt) cc_final: 0.8467 (tppt)
REVERT: F   15 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6765 (mt)
REVERT: G   41 ASP cc_start: 0.7658 (m-30) cc_final: 0.7349 (m-30)
REVERT: G   62 LYS cc_start: 0.6349 (mppt) cc_final: 0.5930 (mttp)
REVERT: G   67 TYR cc_start: 0.7574 (m-80) cc_final: 0.7315 (m-80)
  outliers start: 15
  outliers final: 5
  residues processed: 117
  average time/residue: 1.2975
  time to fit residues: 158.9779
Evaluate side-chains
  118 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 MET
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain D residue   58 SER
Chi-restraints excluded: chain F residue   15 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 45 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 219 ASN
G  36 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.141994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.101097 restraints weight = 7368.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 1.77
r_work: 0.2926 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2783 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.2588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6455  Z= 0.203
  Angle     :  0.523   8.078   8717  Z= 0.270
  Chirality :  0.038   0.133    974
  Planarity :  0.004   0.051   1095
  Dihedral  :  3.930  19.294    833
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 18.48 %
    Favored  : 79.39 %
  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 (0.31), residues: 777
  helix:  2.33 (0.21), residues: 570
  sheet:  None (None), residues: 0
  loop : -0.59 (0.47), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  75 
 HIS   0.003   0.001   HIS G  36 
 PHE   0.015   0.001   PHE G  55 
 TYR   0.013   0.001   TYR A  80 
 ARG   0.014   0.001   ARG A 218 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.761 
Fit side-chains
REVERT: A   30 LYS cc_start: 0.7559 (tmmt) cc_final: 0.6988 (ttmm)
REVERT: A   34 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7481 (mm-30)
REVERT: A   38 LYS cc_start: 0.8142 (mmmt) cc_final: 0.7257 (mmtp)
REVERT: A   48 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8365 (mtt)
REVERT: A   59 GLN cc_start: 0.7608 (mt0) cc_final: 0.6892 (mp10)
REVERT: A   84 LYS cc_start: 0.7971 (tttp) cc_final: 0.7626 (ttmp)
REVERT: A   87 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8232 (m-30)
REVERT: A  162 MET cc_start: 0.8139 (pp-130) cc_final: 0.7841 (ppp)
REVERT: A  164 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7418 (pt0)
REVERT: A  214 SER cc_start: 0.8059 (m) cc_final: 0.7618 (p)
REVERT: A  217 GLN cc_start: 0.8055 (tt0) cc_final: 0.7164 (pt0)
REVERT: B   34 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7274 (mm-30)
REVERT: B  113 ARG cc_start: 0.7084 (mtt180) cc_final: 0.6552 (mtt90)
REVERT: B  126 TYR cc_start: 0.7939 (t80) cc_final: 0.7499 (t80)
REVERT: B  131 GLU cc_start: 0.7142 (mp0) cc_final: 0.6792 (mp0)
REVERT: B  139 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.6592 (ttm-80)
REVERT: E   25 ILE cc_start: 0.8847 (mm) cc_final: 0.8568 (mt)
REVERT: E   33 LYS cc_start: 0.8747 (tptt) cc_final: 0.8476 (tppt)
REVERT: F   15 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6806 (mt)
REVERT: G   41 ASP cc_start: 0.7670 (m-30) cc_final: 0.7339 (m-30)
REVERT: G   62 LYS cc_start: 0.6359 (mppt) cc_final: 0.5932 (mttp)
REVERT: G   67 TYR cc_start: 0.7602 (m-80) cc_final: 0.7357 (m-80)
  outliers start: 14
  outliers final: 6
  residues processed: 115
  average time/residue: 1.2886
  time to fit residues: 155.2343
Evaluate side-chains
  115 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 MET
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain D residue   58 SER
Chi-restraints excluded: chain F residue   15 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 32 optimal weight:    0.3980
   chunk 7 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 27 optimal weight:    8.9990
   chunk 55 optimal weight:    0.4980
   chunk 64 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 219 ASN
B  85 GLN
B 148 ASN
G  36 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.143141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.101974 restraints weight = 7396.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 1.78
r_work: 0.2942 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2798 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.2657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6455  Z= 0.167
  Angle     :  0.512   9.233   8717  Z= 0.264
  Chirality :  0.037   0.131    974
  Planarity :  0.004   0.056   1095
  Dihedral  :  3.862  18.872    833
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 18.79 %
    Favored  : 79.70 %
  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:  2.47 (0.31), residues: 777
  helix:  2.40 (0.21), residues: 571
  sheet:  None (None), residues: 0
  loop : -0.57 (0.47), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP B  75 
 HIS   0.002   0.001   HIS E  36 
 PHE   0.017   0.001   PHE E  55 
 TYR   0.013   0.001   TYR A  80 
 ARG   0.016   0.001   ARG A 218 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.669 
Fit side-chains
REVERT: A   30 LYS cc_start: 0.7546 (tmmt) cc_final: 0.6981 (ttmm)
REVERT: A   34 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7464 (mm-30)
REVERT: A   38 LYS cc_start: 0.8140 (mmmt) cc_final: 0.7265 (mmtp)
REVERT: A   48 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8370 (mtt)
REVERT: A   59 GLN cc_start: 0.7526 (mt0) cc_final: 0.6891 (mp10)
REVERT: A   84 LYS cc_start: 0.7938 (tttp) cc_final: 0.7675 (ttmp)
REVERT: A   87 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8306 (m-30)
REVERT: A  162 MET cc_start: 0.8099 (pp-130) cc_final: 0.7837 (ppp)
REVERT: A  164 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7370 (pt0)
REVERT: A  214 SER cc_start: 0.8015 (m) cc_final: 0.7605 (p)
REVERT: A  217 GLN cc_start: 0.8071 (tt0) cc_final: 0.7199 (pt0)
REVERT: B   34 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7258 (mm-30)
REVERT: B  113 ARG cc_start: 0.7133 (mtt180) cc_final: 0.6574 (mtt90)
REVERT: B  126 TYR cc_start: 0.7916 (t80) cc_final: 0.7509 (t80)
REVERT: B  131 GLU cc_start: 0.7177 (mp0) cc_final: 0.6855 (mp0)
REVERT: B  139 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.6656 (ttm-80)
REVERT: E   10 LYS cc_start: 0.7402 (mtpp) cc_final: 0.6906 (mtmm)
REVERT: E   25 ILE cc_start: 0.8834 (mm) cc_final: 0.8548 (mt)
REVERT: E   33 LYS cc_start: 0.8756 (tptt) cc_final: 0.8495 (tppt)
REVERT: F   15 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6783 (mt)
REVERT: G   41 ASP cc_start: 0.7648 (m-30) cc_final: 0.7332 (m-30)
REVERT: G   62 LYS cc_start: 0.6310 (mppt) cc_final: 0.5870 (mttp)
REVERT: G   67 TYR cc_start: 0.7546 (m-80) cc_final: 0.7295 (m-80)
  outliers start: 10
  outliers final: 6
  residues processed: 111
  average time/residue: 1.2133
  time to fit residues: 141.3979
Evaluate side-chains
  112 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 MET
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain D residue   58 SER
Chi-restraints excluded: chain F residue   15 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0970
   chunk 31 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 48 optimal weight:    0.4980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 219 ASN
B  85 GLN
G  36 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.144251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.103087 restraints weight = 7429.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 1.78
r_work: 0.2948 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2804 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.2700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6455  Z= 0.169
  Angle     :  0.510   7.420   8717  Z= 0.263
  Chirality :  0.037   0.130    974
  Planarity :  0.004   0.059   1095
  Dihedral  :  3.863  18.839    833
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 18.64 %
    Favored  : 79.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.47 (0.31), residues: 777
  helix:  2.40 (0.21), residues: 573
  sheet:  None (None), residues: 0
  loop : -0.61 (0.47), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP B  75 
 HIS   0.002   0.001   HIS E  36 
 PHE   0.016   0.001   PHE E  55 
 TYR   0.014   0.001   TYR A  80 
 ARG   0.015   0.001   ARG A 218 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5061.34 seconds
wall clock time: 86 minutes 57.19 seconds (5217.19 seconds total)