Starting phenix.real_space_refine
on Tue Feb 11 08:29:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6hu7_0273/02_2025/6hu7_0273.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6hu7_0273/02_2025/6hu7_0273.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6hu7_0273/02_2025/6hu7_0273.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6hu7_0273/02_2025/6hu7_0273.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6hu7_0273/02_2025/6hu7_0273.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6hu7_0273/02_2025/6hu7_0273.cif"
  }
  resolution = 2.8
  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=   0.079 sd=   1.306
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      27      5.16       5
     C    3155      2.51       5
     N     820      2.21       5
     O     888      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4890
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "B"
      Number of atoms: 1218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 152, 1218
          Classifications: {'peptide': 152}
          Link IDs: {'PTRANS': 12, 'TRANS': 139}
    Chain: "A"
      Number of atoms: 1190
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 147, 1171
          Classifications: {'peptide': 147}
          Link IDs: {'PTRANS': 12, 'TRANS': 134}
      Conformer: "B"
        Number of residues, atoms: 147, 1171
          Classifications: {'peptide': 147}
          Link IDs: {'PTRANS': 12, 'TRANS': 134}
          bond proxies already assigned to first conformer: 1185
    Chain: "C"
      Number of atoms: 1218
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 151, 1207
          Classifications: {'peptide': 151}
          Link IDs: {'PTRANS': 12, 'TRANS': 138}
      Conformer: "B"
        Number of residues, atoms: 151, 1207
          Classifications: {'peptide': 151}
          Link IDs: {'PTRANS': 12, 'TRANS': 138}
          bond proxies already assigned to first conformer: 1230
    Chain: "D"
      Number of atoms: 1207
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 1207
          Classifications: {'peptide': 151}
          Link IDs: {'PTRANS': 12, 'TRANS': 138}
    Chain: "F"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 15
          Classifications: {'peptide': 2}
          Link IDs: {'TRANS': 1}
    Chain: "G"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 21
          Classifications: {'peptide': 3}
          Link IDs: {'TRANS': 2}
    Chain: "H"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 21
          Classifications: {'peptide': 3}
          Link IDs: {'TRANS': 2}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AARG A 127 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 127 " occ=0.50
    residue:
      pdb=" N  AARG C  82 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG C  82 " occ=0.50
  Time building chain proxies: 7.50, per 1000 atoms: 1.53
  Number of scatterers: 4890
  At special positions: 0
  Unit cell: (107.712, 117.216, 81.312, 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      27     16.00
     O     888      8.00
     N     820      7.00
     C    3155      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: 1.19
  Conformation dependent library (CDL) restraints added in 880.4 milliseconds
  

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1176

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 0 sheets defined
      73.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 10
    Processing helix  chain 'B' and resid 12 through 17
    Processing helix  chain 'B' and resid 18 through 19
      No H-bonds generated for 'chain 'B' and resid 18 through 19'
    Processing helix  chain 'B' and resid 20 through 24
    Processing helix  chain 'B' and resid 26 through 43
      removed outlier: 3.585A  pdb=" N   ARG B  39 " --> pdb=" O   SER B  35 " (cutoff:3.500A)
      removed outlier: 7.387A  pdb=" N   GLU B  40 " --> pdb=" O   ALA B  36 " (cutoff:3.500A)
      removed outlier: 5.821A  pdb=" N   ALA B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 75
      removed outlier: 3.718A  pdb=" N   GLY B  73 " --> pdb=" O   ALA B  69 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   VAL B  74 " --> pdb=" O   THR B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 110
      removed outlier: 3.654A  pdb=" N   ASP B  83 " --> pdb=" O   PRO B  79 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   LEU B  84 " --> pdb=" O   ALA B  80 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   TYR B  88 " --> pdb=" O   LEU B  84 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   MET B  93 " --> pdb=" O   VAL B  89 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLY B  94 " --> pdb=" O   ASN B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 128
    Processing helix  chain 'A' and resid 6 through 10
    Processing helix  chain 'A' and resid 20 through 24
      removed outlier: 3.822A  pdb=" N   PHE A  24 " --> pdb=" O   SER A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 38
    Processing helix  chain 'A' and resid 38 through 43
    Processing helix  chain 'A' and resid 49 through 76
      removed outlier: 3.545A  pdb=" N   LEU A  76 " --> pdb=" O   VAL A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 111
      removed outlier: 3.507A  pdb=" N   ASP A  83 " --> pdb=" O   PRO A  79 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   LEU A  84 " --> pdb=" O   ALA A  80 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   MET A  93 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   GLY A  94 " --> pdb=" O   ASN A  90 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   LYS A  96 " --> pdb=" O   ASN A  92 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU A  97 " --> pdb=" O   MET A  93 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU A 100 " --> pdb=" O   LYS A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 128
    Processing helix  chain 'C' and resid 6 through 10
    Processing helix  chain 'C' and resid 12 through 17
      removed outlier: 3.588A  pdb=" N   LEU C  16 " --> pdb=" O   THR C  12 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 43
      removed outlier: 3.639A  pdb=" N   ARG C  39 " --> pdb=" O   SER C  35 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   GLU C  40 " --> pdb=" O   ALA C  36 " (cutoff:3.500A)
      removed outlier: 5.828A  pdb=" N   ALA C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 49 through 76
    Processing helix  chain 'C' and resid 78 through 91
      removed outlier: 3.523A  pdb=" N   LEU C  84 " --> pdb=" O   ALA C  80 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   VAL C  85 " --> pdb=" O   SER C  81 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 111
      removed outlier: 3.831A  pdb=" N   LYS C  96 " --> pdb=" O   ASN C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 128
      removed outlier: 3.573A  pdb=" N   ARG C 127 " --> pdb=" O   GLY C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 133
    Processing helix  chain 'D' and resid 6 through 10
    Processing helix  chain 'D' and resid 20 through 24
      removed outlier: 3.760A  pdb=" N   PHE D  24 " --> pdb=" O   SER D  21 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 26 through 38
    Processing helix  chain 'D' and resid 38 through 43
    Processing helix  chain 'D' and resid 49 through 76
      removed outlier: 3.553A  pdb=" N   GLY D  73 " --> pdb=" O   ALA D  69 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 91
      removed outlier: 3.505A  pdb=" N   ASP D  83 " --> pdb=" O   PRO D  79 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LEU D  84 " --> pdb=" O   ALA D  80 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   SER D  87 " --> pdb=" O   ASP D  83 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 91 through 109
      removed outlier: 4.131A  pdb=" N   LYS D  96 " --> pdb=" O   ASN D  92 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LEU D  97 " --> pdb=" O   MET D  93 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   THR D 109 " --> pdb=" O   ILE D 105 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 111 through 128
      removed outlier: 3.570A  pdb=" N   THR D 128 " --> pdb=" O   VAL D 124 " (cutoff:3.500A)

    299 hydrogen bonds defined for protein.
    857 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: 1.30

  Time building geometry restraints manager: 1.39 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: 1564
        1.34 -     1.46: 1067
        1.46 -     1.57: 2360
        1.57 -     1.69: 0
        1.69 -     1.81: 39
  Bond restraints: 5030
  Sorted by residual:
  bond pdb=" CG  LEU A  97 "
       pdb=" CD2 LEU A  97 "
    ideal  model  delta    sigma   weight residual
    1.521  1.459  0.062 3.30e-02 9.18e+02 3.58e+00
  bond pdb=" CG  LEU C  30 "
       pdb=" CD1 LEU C  30 "
    ideal  model  delta    sigma   weight residual
    1.521  1.462  0.059 3.30e-02 9.18e+02 3.16e+00
  bond pdb=" CG  LEU D  97 "
       pdb=" CD2 LEU D  97 "
    ideal  model  delta    sigma   weight residual
    1.521  1.466  0.055 3.30e-02 9.18e+02 2.78e+00
  bond pdb=" CB  GLU B   8 "
       pdb=" CG  GLU B   8 "
    ideal  model  delta    sigma   weight residual
    1.520  1.476  0.044 3.00e-02 1.11e+03 2.11e+00
  bond pdb=" CB  ARG A  98 "
       pdb=" CG  ARG A  98 "
    ideal  model  delta    sigma   weight residual
    1.520  1.477  0.043 3.00e-02 1.11e+03 2.04e+00
  ... (remaining 5025 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 6611
        1.80 -     3.61: 238
        3.61 -     5.41: 25
        5.41 -     7.21: 7
        7.21 -     9.02: 3
  Bond angle restraints: 6884
  Sorted by residual:
  angle pdb=" CA  TYR A  38 "
        pdb=" CB  TYR A  38 "
        pdb=" CG  TYR A  38 "
      ideal   model   delta    sigma   weight residual
     113.90  107.49    6.41 1.80e+00 3.09e-01 1.27e+01
  angle pdb=" CA  TYR C 132 "
        pdb=" CB  TYR C 132 "
        pdb=" CG  TYR C 132 "
      ideal   model   delta    sigma   weight residual
     113.90  108.31    5.59 1.80e+00 3.09e-01 9.65e+00
  angle pdb=" CA  TYR D  38 "
        pdb=" CB  TYR D  38 "
        pdb=" CG  TYR D  38 "
      ideal   model   delta    sigma   weight residual
     113.90  108.53    5.37 1.80e+00 3.09e-01 8.89e+00
  angle pdb=" C   VAL C 148 "
        pdb=" N   VAL C 149 "
        pdb=" CA  VAL C 149 "
      ideal   model   delta    sigma   weight residual
     121.97  126.98   -5.01 1.80e+00 3.09e-01 7.75e+00
  angle pdb=" C   MET D   1 "
        pdb=" N   ASP D   2 "
        pdb=" CA  ASP D   2 "
      ideal   model   delta    sigma   weight residual
     122.46  126.24   -3.78 1.41e+00 5.03e-01 7.20e+00
  ... (remaining 6879 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.70: 2873
       15.70 -    31.39: 92
       31.39 -    47.08: 27
       47.08 -    62.78: 1
       62.78 -    78.47: 5
  Dihedral angle restraints: 2998
    sinusoidal: 1194
      harmonic: 1804
  Sorted by residual:
  dihedral pdb=" CA  LEU A 143 "
           pdb=" C   LEU A 143 "
           pdb=" N   PRO A 144 "
           pdb=" CA  PRO A 144 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.27   25.73     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" CA  LEU D 108 "
           pdb=" C   LEU D 108 "
           pdb=" N   THR D 109 "
           pdb=" CA  THR D 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.50   20.50     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  LEU B 143 "
           pdb=" C   LEU B 143 "
           pdb=" N   PRO B 144 "
           pdb=" CA  PRO B 144 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.98   19.02     0      5.00e+00 4.00e-02 1.45e+01
  ... (remaining 2995 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 537
       0.047 -    0.094: 203
       0.094 -    0.141: 42
       0.141 -    0.187: 7
       0.187 -    0.234: 1
  Chirality restraints: 790
  Sorted by residual:
  chirality pdb=" CG  LEU A  97 "
            pdb=" CB  LEU A  97 "
            pdb=" CD1 LEU A  97 "
            pdb=" CD2 LEU A  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" CA  HIS A  47 "
            pdb=" N   HIS A  47 "
            pdb=" C   HIS A  47 "
            pdb=" CB  HIS A  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.81e-01
  chirality pdb=" CB  THR D 109 "
            pdb=" CA  THR D 109 "
            pdb=" OG1 THR D 109 "
            pdb=" CG2 THR D 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.39e-01
  ... (remaining 787 not shown)

  Planarity restraints: 872
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C  18 "   -0.026 2.00e-02 2.50e+03   2.28e-02 9.12e+00
        pdb=" CG  PHE C  18 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 PHE C  18 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE C  18 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE C  18 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE C  18 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE C  18 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 132 "    0.025 2.00e-02 2.50e+03   2.05e-02 8.44e+00
        pdb=" CG  TYR C 132 "   -0.050 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 132 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 132 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 132 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 132 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 132 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR C 132 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  38 "   -0.028 2.00e-02 2.50e+03   1.89e-02 7.11e+00
        pdb=" CG  TYR A  38 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  38 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  38 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  38 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  38 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  38 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR A  38 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 869 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 71
        2.68 -     3.24: 4989
        3.24 -     3.79: 7768
        3.79 -     4.35: 10897
        4.35 -     4.90: 17311
  Nonbonded interactions: 41036
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG B 150 "
            pdb=" O   LEU C 143 "
     model   vdw
     2.130 3.120
  nonbonded pdb=" OD1 ASP A   2 "
            pdb=" N   ILE A   3 "
     model   vdw
     2.165 3.120
  nonbonded pdb=" O   THR B 146 "
            pdb=" OG1 THR B 147 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   PHE D  24 "
            pdb=" NH1 ARG D  98 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" OD1 ASP A  83 "
            pdb=" N   LEU A  84 "
     model   vdw
     2.314 3.120
  ... (remaining 41031 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 1 through 27 or resid 29 through 81 or resid 83 through 12 \ 
6 or resid 128 through 147))
  selection = (chain 'B' and (resid 1 through 27 or resid 29 through 81 or resid 83 through 12 \ 
6 or resid 128 through 147))
  selection = (chain 'C' and (resid 1 through 27 or resid 29 through 81 or resid 83 through 12 \ 
6 or resid 128 through 147))
  selection = (chain 'D' and (resid 1 through 27 or resid 29 through 81 or resid 83 through 12 \ 
6 or resid 128 through 147))
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.99
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:             8.890
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     20.010
  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:15.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.071   5030  Z= 0.520
  Angle     :  0.781   9.018   6884  Z= 0.411
  Chirality :  0.050   0.234    790
  Planarity :  0.007   0.060    872
  Dihedral  :  9.806  78.470   1822
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  2.69 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  0.36 %
    Favored  : 99.27 %
  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: -3.47 (0.28), residues: 602
  helix: -3.23 (0.16), residues: 405
  sheet:  None (None), residues: 0
  loop :  0.50 (0.43), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 102 
 HIS   0.014   0.004   HIS A  47 
 PHE   0.053   0.003   PHE C  18 
 TYR   0.050   0.006   TYR C 132 
 ARG   0.011   0.002   ARG A  56 

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.579 
Fit side-chains
REVERT: B   61 CYS cc_start: 0.8966 (t) cc_final: 0.8723 (t)
REVERT: B   82 ARG cc_start: 0.6554 (mtp180) cc_final: 0.5565 (ptt-90)
REVERT: B  117 GLU cc_start: 0.8095 (tt0) cc_final: 0.7722 (tp30)
REVERT: A   64 GLU cc_start: 0.6708 (tp30) cc_final: 0.6467 (mm-30)
REVERT: A  117 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8486 (mm-30)
REVERT: A  141 SER cc_start: 0.8697 (m) cc_final: 0.8441 (m)
REVERT: C   83 ASP cc_start: 0.7576 (m-30) cc_final: 0.7194 (m-30)
REVERT: C  113 GLU cc_start: 0.7977 (pm20) cc_final: 0.7764 (mp0)
REVERT: D   64 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7845 (mm-30)
REVERT: D   78 ASP cc_start: 0.7218 (t0) cc_final: 0.6891 (t0)
REVERT: D   96 LYS cc_start: 0.8524 (mtpp) cc_final: 0.8281 (mtpt)
REVERT: D  136 ASN cc_start: 0.7122 (p0) cc_final: 0.6851 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 1.5119
  time to fit residues: 188.7167
Evaluate side-chains
  95 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 30 optimal weight:   10.0000
   chunk 23 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 17 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B  52 HIS
B  57 GLN
B  75 ASN
B  90 ASN
B 104 HIS
A  47 HIS
A  52 HIS
A  57 GLN
A  75 ASN
A 136 ASN
C  52 HIS
C  75 ASN
D  47 HIS
D  52 HIS
D  90 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.113903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.097456 restraints weight = 17302.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 2.06
r_work: 0.2968 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2879
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5030  Z= 0.223
  Angle     :  0.673   9.158   6884  Z= 0.341
  Chirality :  0.042   0.239    790
  Planarity :  0.007   0.044    872
  Dihedral  :  5.209  23.067    670
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  1.68 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  :  8.21 %
    Favored  : 89.78 %
  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:  0.15 (0.33), residues: 602
  helix: -0.19 (0.24), residues: 406
  sheet:  None (None), residues: 0
  loop :  1.22 (0.45), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 102 
 HIS   0.006   0.002   HIS B  47 
 PHE   0.032   0.002   PHE C  18 
 TYR   0.028   0.003   TYR C 132 
 ARG   0.008   0.001   ARG C  39 

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.600 
Fit side-chains
REVERT: B   76 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7278 (tt)
REVERT: B  117 GLU cc_start: 0.8629 (tt0) cc_final: 0.8267 (mm-30)
REVERT: A   32 ASP cc_start: 0.8836 (m-30) cc_final: 0.8531 (m-30)
REVERT: A   79 PRO cc_start: 0.7958 (Cg_endo) cc_final: 0.7695 (Cg_exo)
REVERT: D   64 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8608 (mm-30)
REVERT: D   98 ARG cc_start: 0.8628 (ptt90) cc_final: 0.8373 (ptt-90)
  outliers start: 9
  outliers final: 3
  residues processed: 106
  average time/residue: 1.4643
  time to fit residues: 160.4651
Evaluate side-chains
  92 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  142 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 48 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
B  99 GLN
A 136 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.114292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.098049 restraints weight = 17036.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 2.04
r_work: 0.3003 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2909 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2909
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2909
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5030  Z= 0.223
  Angle     :  0.613   8.770   6884  Z= 0.305
  Chirality :  0.040   0.214    790
  Planarity :  0.006   0.041    872
  Dihedral  :  4.824  20.469    670
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  1.85 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 10.95 %
    Favored  : 87.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.46 (0.34), residues: 602
  helix:  0.98 (0.25), residues: 406
  sheet:  None (None), residues: 0
  loop :  1.32 (0.45), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 102 
 HIS   0.003   0.001   HIS D  47 
 PHE   0.026   0.002   PHE C  18 
 TYR   0.025   0.002   TYR C 132 
 ARG   0.004   0.001   ARG A  98 

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.540 
Fit side-chains
REVERT: B   14 GLU cc_start: 0.8987 (mp0) cc_final: 0.8581 (mt-10)
REVERT: B   76 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7469 (tt)
REVERT: B  117 GLU cc_start: 0.8588 (tt0) cc_final: 0.8303 (mm-30)
REVERT: A   32 ASP cc_start: 0.8802 (m-30) cc_final: 0.8501 (m-30)
REVERT: C   28 ARG cc_start: 0.7976 (mmm160) cc_final: 0.7398 (mmm160)
REVERT: C   32 ASP cc_start: 0.8915 (m-30) cc_final: 0.8638 (m-30)
REVERT: D   98 ARG cc_start: 0.8534 (ptt90) cc_final: 0.8295 (ptt-90)
  outliers start: 7
  outliers final: 4
  residues processed: 93
  average time/residue: 1.4640
  time to fit residues: 140.6306
Evaluate side-chains
  90 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  142 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 13 optimal weight:    0.0000
   chunk 38 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0980
   chunk 55 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0570
   chunk 39 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.3902

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

Flipped N/Q/H residues before XYZ refinement:
** B  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 104 HIS
A 136 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.116083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.100083 restraints weight = 15475.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 1.98
r_work: 0.3039 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2932
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2933 r_free = 0.2933    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2933
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.2995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5030  Z= 0.155
  Angle     :  0.552   8.346   6884  Z= 0.272
  Chirality :  0.037   0.170    790
  Planarity :  0.005   0.038    872
  Dihedral  :  4.488  18.884    670
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  1.68 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 11.86 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.34), residues: 602
  helix:  1.49 (0.26), residues: 410
  sheet:  None (None), residues: 0
  loop :  1.53 (0.47), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 102 
 HIS   0.003   0.001   HIS B  47 
 PHE   0.019   0.001   PHE C  18 
 TYR   0.018   0.001   TYR C 132 
 ARG   0.003   0.000   ARG A  98 

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.533 
Fit side-chains
REVERT: B   14 GLU cc_start: 0.9133 (mp0) cc_final: 0.8761 (mt-10)
REVERT: B   76 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7353 (tt)
REVERT: B   83 ASP cc_start: 0.7883 (m-30) cc_final: 0.7495 (p0)
REVERT: B  117 GLU cc_start: 0.8507 (tt0) cc_final: 0.8207 (mm-30)
  outliers start: 6
  outliers final: 2
  residues processed: 97
  average time/residue: 1.3726
  time to fit residues: 137.8199
Evaluate side-chains
  83 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  143 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 4 optimal weight:    0.0770
   chunk 25 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0000
   chunk 7 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0980
   chunk 57 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.4346

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

Flipped N/Q/H residues before XYZ refinement:
B  99 GLN
D 104 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.116779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.099734 restraints weight = 22747.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 2.42
r_work: 0.3020 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3011
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3011
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.3138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5030  Z= 0.159
  Angle     :  0.546   7.769   6884  Z= 0.269
  Chirality :  0.037   0.177    790
  Planarity :  0.005   0.035    872
  Dihedral  :  4.344  17.115    670
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  1.51 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 13.87 %
    Favored  : 84.67 %
  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:  2.41 (0.34), residues: 602
  helix:  1.72 (0.26), residues: 410
  sheet:  None (None), residues: 0
  loop :  1.61 (0.46), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  62 
 HIS   0.003   0.001   HIS B 104 
 PHE   0.017   0.001   PHE C  18 
 TYR   0.017   0.001   TYR C 132 
 ARG   0.002   0.000   ARG A  98 

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.581 
Fit side-chains
REVERT: B   14 GLU cc_start: 0.8745 (mp0) cc_final: 0.8463 (mt-10)
REVERT: B   76 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7295 (tt)
REVERT: B   83 ASP cc_start: 0.7815 (m-30) cc_final: 0.7426 (p0)
REVERT: B   97 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8889 (tm)
REVERT: C   32 ASP cc_start: 0.8800 (m-30) cc_final: 0.8588 (m-30)
  outliers start: 6
  outliers final: 2
  residues processed: 90
  average time/residue: 1.4564
  time to fit residues: 135.5071
Evaluate side-chains
  83 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  146 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0470
   chunk 10 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.7278

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.116137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.100736 restraints weight = 12663.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 1.77
r_work: 0.3064 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2941
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2941
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.3242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5030  Z= 0.180
  Angle     :  0.566   7.593   6884  Z= 0.280
  Chirality :  0.038   0.174    790
  Planarity :  0.005   0.034    872
  Dihedral  :  4.287  15.931    670
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  2.18 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 13.32 %
    Favored  : 84.49 %
  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:  2.54 (0.35), residues: 602
  helix:  1.85 (0.26), residues: 409
  sheet:  None (None), residues: 0
  loop :  1.60 (0.46), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  62 
 HIS   0.004   0.001   HIS B 104 
 PHE   0.019   0.001   PHE C  18 
 TYR   0.019   0.002   TYR C 132 
 ARG   0.003   0.000   ARG A  98 

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.543 
Fit side-chains
REVERT: B   14 GLU cc_start: 0.8848 (mp0) cc_final: 0.8583 (mt-10)
REVERT: B   76 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7409 (tt)
REVERT: B   97 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8929 (tm)
REVERT: C   28 ARG cc_start: 0.7997 (mmm160) cc_final: 0.7523 (mmm160)
REVERT: C   32 ASP cc_start: 0.8886 (m-30) cc_final: 0.8682 (m-30)
  outliers start: 10
  outliers final: 4
  residues processed: 96
  average time/residue: 1.4616
  time to fit residues: 145.0108
Evaluate side-chains
  89 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  142 THR
Chi-restraints excluded: chain D residue  146 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.115371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.098474 restraints weight = 24748.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 2.47
r_work: 0.2994 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2987
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2987 r_free = 0.2987    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2987 r_free = 0.2987    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2987
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.3273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5030  Z= 0.197
  Angle     :  0.572   7.418   6884  Z= 0.283
  Chirality :  0.038   0.165    790
  Planarity :  0.005   0.034    872
  Dihedral  :  4.293  14.914    670
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  2.18 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.32 %
    Favored  : 84.85 %
  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:  2.56 (0.35), residues: 602
  helix:  1.87 (0.26), residues: 409
  sheet:  None (None), residues: 0
  loop :  1.59 (0.47), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  62 
 HIS   0.004   0.001   HIS B 104 
 PHE   0.019   0.001   PHE C  18 
 TYR   0.020   0.002   TYR C 132 
 ARG   0.003   0.000   ARG A  56 

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.516 
Fit side-chains
REVERT: B   14 GLU cc_start: 0.8752 (mp0) cc_final: 0.8549 (mt-10)
REVERT: B   76 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7364 (tt)
REVERT: B   97 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8958 (tm)
REVERT: C   28 ARG cc_start: 0.7970 (mmm160) cc_final: 0.6932 (tpm170)
REVERT: C   32 ASP cc_start: 0.8781 (m-30) cc_final: 0.8459 (m-30)
  outliers start: 8
  outliers final: 4
  residues processed: 94
  average time/residue: 1.4268
  time to fit residues: 138.6732
Evaluate side-chains
  92 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  142 THR
Chi-restraints excluded: chain D residue  146 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 8 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.115777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.099453 restraints weight = 19460.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 2.19
r_work: 0.3011 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2907
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2907 r_free = 0.2907    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2907 r_free = 0.2907    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2907
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.3380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5030  Z= 0.186
  Angle     :  0.565   7.214   6884  Z= 0.279
  Chirality :  0.038   0.164    790
  Planarity :  0.005   0.034    872
  Dihedral  :  4.265  14.374    670
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  2.18 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 13.32 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.61 (0.35), residues: 602
  helix:  1.93 (0.26), residues: 409
  sheet:  None (None), residues: 0
  loop :  1.55 (0.47), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  62 
 HIS   0.004   0.001   HIS B 104 
 PHE   0.018   0.001   PHE C  18 
 TYR   0.018   0.002   TYR C 132 
 ARG   0.002   0.000   ARG A  98 

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.488 
Fit side-chains
REVERT: B   14 GLU cc_start: 0.8927 (mp0) cc_final: 0.8691 (mt-10)
REVERT: B   76 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7551 (tt)
REVERT: C   28 ARG cc_start: 0.8183 (mmm160) cc_final: 0.7563 (tpm170)
  outliers start: 6
  outliers final: 4
  residues processed: 95
  average time/residue: 1.4916
  time to fit residues: 146.5870
Evaluate side-chains
  95 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  142 THR
Chi-restraints excluded: chain D residue  146 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 52 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0270
   chunk 51 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0570
   chunk 8 optimal weight:    6.9990
   overall best weight:    0.4756

-------------------------------------------------------------------------------
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 = 0.3371 r_free = 0.3371 target = 0.117355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.100491 restraints weight = 25595.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3123 rms_B_bonded: 2.54
r_work: 0.3011 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3019
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3019 r_free = 0.3019    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3019 r_free = 0.3019    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3019
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.3507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   5030  Z= 0.159
  Angle     :  0.557   7.304   6884  Z= 0.272
  Chirality :  0.037   0.174    790
  Planarity :  0.005   0.033    872
  Dihedral  :  4.180  14.180    670
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  2.35 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.87 %
    Favored  : 84.31 %
  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:  2.71 (0.35), residues: 602
  helix:  2.00 (0.26), residues: 409
  sheet:  None (None), residues: 0
  loop :  1.60 (0.47), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  62 
 HIS   0.003   0.001   HIS B 104 
 PHE   0.016   0.001   PHE C  18 
 TYR   0.016   0.001   TYR C 132 
 ARG   0.002   0.000   ARG A  98 

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.555 
Fit side-chains
REVERT: B   76 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7140 (tt)
REVERT: B   83 ASP cc_start: 0.7878 (m-30) cc_final: 0.7451 (p0)
REVERT: C   28 ARG cc_start: 0.8024 (mmm160) cc_final: 0.7433 (tpm170)
REVERT: C   83 ASP cc_start: 0.8014 (m-30) cc_final: 0.7788 (m-30)
  outliers start: 8
  outliers final: 5
  residues processed: 98
  average time/residue: 1.4593
  time to fit residues: 148.0199
Evaluate side-chains
  92 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  142 THR
Chi-restraints excluded: chain D residue  146 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0050
   chunk 43 optimal weight:    3.9990
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
B  47 HIS
D  92 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.115631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.098936 restraints weight = 18964.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3120 rms_B_bonded: 2.22
r_work: 0.3020 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2902
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2902 r_free = 0.2902    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2902 r_free = 0.2902    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2902
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.3536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5030  Z= 0.176
  Angle     :  0.569   7.519   6884  Z= 0.279
  Chirality :  0.038   0.163    790
  Planarity :  0.005   0.034    872
  Dihedral  :  4.170  14.032    670
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  2.18 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 14.60 %
    Favored  : 83.76 %
  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:  2.72 (0.35), residues: 602
  helix:  2.01 (0.26), residues: 409
  sheet:  None (None), residues: 0
  loop :  1.59 (0.47), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 102 
 HIS   0.004   0.001   HIS B  47 
 PHE   0.017   0.001   PHE C  18 
 TYR   0.017   0.001   TYR C 132 
 ARG   0.002   0.000   ARG A  98 

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.555 
Fit side-chains
REVERT: B   76 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7281 (tt)
REVERT: B   83 ASP cc_start: 0.8050 (m-30) cc_final: 0.7567 (p0)
REVERT: C   28 ARG cc_start: 0.8166 (mmm160) cc_final: 0.7531 (tpm170)
REVERT: C   66 MET cc_start: 0.8802 (mmp) cc_final: 0.8550 (mmp)
REVERT: C   83 ASP cc_start: 0.8096 (m-30) cc_final: 0.7861 (m-30)
  outliers start: 7
  outliers final: 6
  residues processed: 98
  average time/residue: 1.4341
  time to fit residues: 145.2745
Evaluate side-chains
  96 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain D residue  142 THR
Chi-restraints excluded: chain D residue  146 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 53 optimal weight:    0.0980
   chunk 51 optimal weight:    3.9990
   chunk 27 optimal weight:    0.5980
   chunk 3 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 16 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0270
   chunk 14 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.4038

-------------------------------------------------------------------------------
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 = 0.3387 r_free = 0.3387 target = 0.118595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.102156 restraints weight = 21079.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 2.27
r_work: 0.3033 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2931 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2942
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2942
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.3631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   5030  Z= 0.155
  Angle     :  0.547   7.756   6884  Z= 0.269
  Chirality :  0.037   0.165    790
  Planarity :  0.004   0.033    872
  Dihedral  :  4.100  14.011    670
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  2.18 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 14.78 %
    Favored  : 83.76 %
  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 (0.35), residues: 602
  helix:  2.07 (0.26), residues: 409
  sheet:  None (None), residues: 0
  loop :  1.67 (0.48), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 102 
 HIS   0.003   0.001   HIS B 104 
 PHE   0.015   0.001   PHE C  18 
 TYR   0.015   0.001   TYR C 132 
 ARG   0.002   0.000   ARG A  98 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5184.38 seconds
wall clock time: 92 minutes 47.86 seconds (5567.86 seconds total)