Starting phenix.real_space_refine
on Sat Aug 23 11:29:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6se0_10151/08_2025/6se0_10151.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6se0_10151/08_2025/6se0_10151.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6se0_10151/08_2025/6se0_10151.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6se0_10151/08_2025/6se0_10151.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6se0_10151/08_2025/6se0_10151.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6se0_10151/08_2025/6se0_10151.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     288      5.49       5
     S      10      5.16       5
     C    6657      2.51       5
     N    2256      2.21       5
     O    2791      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12002
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 816
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 2, 'TRANS': 96}
    Chain: "B"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 845
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 5, 'TRANS': 104}
    Chain: "D"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 816
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 2, 'TRANS': 96}
    Chain: "F"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 829
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 4, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 2952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2952
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2987
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 2.50, per 1000 atoms: 0.21
  Number of scatterers: 12002
  At special positions: 0
  Unit cell: (75.26, 119.78, 115.54, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     P     288     15.00
     O    2791      8.00
     N    2256      7.00
     C    6657      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: 0.90
  Conformation dependent library (CDL) restraints added in 241.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1414

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 9 sheets defined
      70.8% alpha, 2.6% beta
      145 base pairs and 257 stacking pairs defined.
    Time for finding SS restraints: 1.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 57
      removed outlier: 3.806A  pdb=" N   GLU A  50 " --> pdb=" O   GLY A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.824A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LYS A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 116
      removed outlier: 3.509A  pdb=" N   ALA A 116 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 133
    Processing helix  chain 'A' and resid 134 through 139
      removed outlier: 3.783A  pdb=" N   LEU A 139 " --> pdb=" O   LEU A 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.593A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.202A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.583A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 46 through 73
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.616A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 98
      removed outlier: 3.700A  pdb=" N   LEU C  96 " --> pdb=" O   GLU C  92 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.664A  pdb=" N   VAL D  41 " --> pdb=" O   TYR D  37 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.547A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.520A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU D 102 " --> pdb=" O   VAL D  98 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 122
      removed outlier: 3.522A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.838A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 116
      removed outlier: 3.602A  pdb=" N   LEU E  91 " --> pdb=" O   GLN E  87 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA E 116 " --> pdb=" O   LEU E 112 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 134
      removed outlier: 3.804A  pdb=" N   GLY E 134 " --> pdb=" O   ARG E 130 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.542A  pdb=" N   GLY F  28 " --> pdb=" O   ASN F  25 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.289A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.509A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 38
      removed outlier: 3.799A  pdb=" N   ASN G  38 " --> pdb=" O   LEU G  34 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.550A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  69 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
      removed outlier: 3.582A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.577A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 104 through 122
      removed outlier: 3.591A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LYS H 120 " --> pdb=" O   LYS H 116 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86
      removed outlier: 7.240A  pdb=" N   ASN A  85 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43
      removed outlier: 6.870A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 86
      removed outlier: 7.015A  pdb=" N   ASN E  85 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 120 through 121
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.527A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78

    377 hydrogen bonds defined for protein.
    1119 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      368 hydrogen bonds
      728 hydrogen bond angles
      0 basepair planarities
      145 basepair parallelities
      257 stacking parallelities
  Total time for adding SS restraints: 1.94

  Time building geometry restraints manager: 1.19 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2004
        1.33 -     1.45: 4338
        1.45 -     1.57: 5874
        1.57 -     1.68: 576
        1.68 -     1.80: 18
  Bond restraints: 12810
  Sorted by residual:
  bond pdb=" C3'  DA J   6 "
       pdb=" O3'  DA J   6 "
    ideal  model  delta    sigma   weight residual
    1.422  1.358  0.064 3.00e-02 1.11e+03 4.55e+00
  bond pdb=" SD  MET G  51 "
       pdb=" CE  MET G  51 "
    ideal  model  delta    sigma   weight residual
    1.791  1.738  0.053 2.50e-02 1.60e+03 4.46e+00
  bond pdb=" CG1 ILE A 132 "
       pdb=" CD1 ILE A 132 "
    ideal  model  delta    sigma   weight residual
    1.513  1.441  0.072 3.90e-02 6.57e+02 3.41e+00
  bond pdb=" CB  ILE A  51 "
       pdb=" CG2 ILE A  51 "
    ideal  model  delta    sigma   weight residual
    1.521  1.462  0.059 3.30e-02 9.18e+02 3.23e+00
  bond pdb=" CB  TRP E  86 "
       pdb=" CG  TRP E  86 "
    ideal  model  delta    sigma   weight residual
    1.498  1.444  0.054 3.10e-02 1.04e+03 3.07e+00
  ... (remaining 12805 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.52: 18371
        3.52 -     7.04: 145
        7.04 -    10.57: 17
       10.57 -    14.09: 1
       14.09 -    17.61: 1
  Bond angle restraints: 18535
  Sorted by residual:
  angle pdb=" CA  LEU F  90 "
        pdb=" CB  LEU F  90 "
        pdb=" CG  LEU F  90 "
      ideal   model   delta    sigma   weight residual
     116.30   98.69   17.61 3.50e+00 8.16e-02 2.53e+01
  angle pdb=" CB  MET G  51 "
        pdb=" CG  MET G  51 "
        pdb=" SD  MET G  51 "
      ideal   model   delta    sigma   weight residual
     112.70  126.00  -13.30 3.00e+00 1.11e-01 1.97e+01
  angle pdb=" C   ILE G  87 "
        pdb=" N   ARG G  88 "
        pdb=" CA  ARG G  88 "
      ideal   model   delta    sigma   weight residual
     121.94  114.53    7.41 2.00e+00 2.50e-01 1.37e+01
  angle pdb=" CA  VAL C 107 "
        pdb=" CB  VAL C 107 "
        pdb=" CG1 VAL C 107 "
      ideal   model   delta    sigma   weight residual
     110.40  116.30   -5.90 1.70e+00 3.46e-01 1.21e+01
  angle pdb=" CA  ARG E  43 "
        pdb=" CB  ARG E  43 "
        pdb=" CG  ARG E  43 "
      ideal   model   delta    sigma   weight residual
     114.10  120.97   -6.87 2.00e+00 2.50e-01 1.18e+01
  ... (remaining 18530 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.26: 5109
       29.26 -    58.52: 1726
       58.52 -    87.78: 87
       87.78 -   117.04: 3
      117.04 -   146.30: 1
  Dihedral angle restraints: 6926
    sinusoidal: 4729
      harmonic: 2197
  Sorted by residual:
  dihedral pdb=" CA  ILE B  29 "
           pdb=" C   ILE B  29 "
           pdb=" N   THR B  30 "
           pdb=" CA  THR B  30 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.46  -19.54     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   73.70  146.30     1      3.50e+01 8.16e-04 1.44e+01
  dihedral pdb=" CA  GLN G 112 "
           pdb=" C   GLN G 112 "
           pdb=" N   ALA G 113 "
           pdb=" CA  ALA G 113 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.04  -16.96     0      5.00e+00 4.00e-02 1.15e+01
  ... (remaining 6923 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1514
       0.058 -    0.116: 486
       0.116 -    0.175: 86
       0.175 -    0.233: 9
       0.233 -    0.291: 4
  Chirality restraints: 2099
  Sorted by residual:
  chirality pdb=" CG  LEU G 108 "
            pdb=" CB  LEU G 108 "
            pdb=" CD1 LEU G 108 "
            pdb=" CD2 LEU G 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.30   -0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" P    DG J  50 "
            pdb=" OP1  DG J  50 "
            pdb=" OP2  DG J  50 "
            pdb=" O5'  DG J  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.60   -0.26 2.00e-01 2.50e+01 1.67e+00
  chirality pdb=" CB  ILE D  54 "
            pdb=" CA  ILE D  54 "
            pdb=" CG1 ILE D  54 "
            pdb=" CG2 ILE D  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.62e+00
  ... (remaining 2096 not shown)

  Planarity restraints: 1338
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G  79 "    0.063 5.00e-02 4.00e+02   9.47e-02 1.44e+01
        pdb=" N   PRO G  80 "   -0.164 5.00e-02 4.00e+02
        pdb=" CA  PRO G  80 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO G  80 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C  79 "    0.058 5.00e-02 4.00e+02   8.80e-02 1.24e+01
        pdb=" N   PRO C  80 "   -0.152 5.00e-02 4.00e+02
        pdb=" CA  PRO C  80 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO C  80 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 119 "    0.017 2.00e-02 2.50e+03   3.27e-02 1.07e+01
        pdb=" C   VAL A 119 "   -0.057 2.00e-02 2.50e+03
        pdb=" O   VAL A 119 "    0.020 2.00e-02 2.50e+03
        pdb=" N   THR A 120 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1335 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2322
        2.78 -     3.31: 10081
        3.31 -     3.84: 23976
        3.84 -     4.37: 26839
        4.37 -     4.90: 37586
  Nonbonded interactions: 100804
  Sorted by model distance:
  nonbonded pdb=" OG  SER G  18 "
            pdb=" O   LEU G  23 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O2   DC I -56 "
            pdb=" N2   DG J  56 "
     model   vdw
     2.286 2.496
  nonbonded pdb=" O2   DC I -62 "
            pdb=" N2   DG J  62 "
     model   vdw
     2.299 2.496
  nonbonded pdb=" OH  TYR H  40 "
            pdb=" OP1  DG I  48 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" OG1 THR E 113 "
            pdb=" O   THR E 120 "
     model   vdw
     2.343 3.040
  ... (remaining 100799 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'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 10 through 116)
  selection = (chain 'G' and resid 10 through 116)
}
ncs_group {
  reference = (chain 'D' and resid 31 through 124)
  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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             0.960
  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:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.190
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
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      :  0.009   0.074  12810  Z= 0.378
  Angle     :  1.012  17.610  18535  Z= 0.574
  Chirality :  0.057   0.291   2099
  Planarity :  0.008   0.095   1338
  Dihedral  : 28.079 146.298   5512
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.82 (0.23), residues: 749
  helix: -1.67 (0.17), residues: 511
  sheet:  None (None), residues: 0
  loop : -1.94 (0.31), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  44 
 TYR   0.035   0.004   TYR A 110 
 PHE   0.025   0.004   PHE A  78 
 TRP   0.018   0.002   TRP E  86 
 HIS   0.015   0.003   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00850 (12810)
  covalent geometry    : angle       1.01243 (18535)
  hydrogen bonds       : bond        0.12059 (  745)
  hydrogen bonds       : angle       4.17951 ( 1847)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.9426 (tp30) cc_final: 0.9176 (tp30)
REVERT: A   85 ASN cc_start: 0.8494 (m-40) cc_final: 0.8198 (m-40)
REVERT: B   45 ARG cc_start: 0.7613 (mtm180) cc_final: 0.6389 (ttm110)
REVERT: B   79 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7575 (mtmm)
REVERT: C   56 GLU cc_start: 0.6795 (tt0) cc_final: 0.6575 (tt0)
REVERT: C   57 TYR cc_start: 0.9003 (t80) cc_final: 0.8528 (t80)
REVERT: C   61 GLU cc_start: 0.8731 (tp30) cc_final: 0.8261 (tp30)
REVERT: C   92 GLU cc_start: 0.8295 (tt0) cc_final: 0.7903 (tt0)
REVERT: C   95 LYS cc_start: 0.8448 (ttmt) cc_final: 0.7929 (tppt)
REVERT: D  113 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7848 (mt-10)
REVERT: D  116 LYS cc_start: 0.8782 (ttpp) cc_final: 0.8555 (ttmm)
REVERT: E   49 LYS cc_start: 0.8950 (ptmt) cc_final: 0.8453 (ptmt)
REVERT: E   64 LYS cc_start: 0.7947 (mtpt) cc_final: 0.7371 (tptt)
REVERT: E   73 GLU cc_start: 0.9093 (tp30) cc_final: 0.8453 (tp30)
REVERT: G   71 ARG cc_start: 0.8700 (mmm-85) cc_final: 0.7951 (mtm-85)
REVERT: G   92 GLU cc_start: 0.8177 (tt0) cc_final: 0.7791 (tt0)
REVERT: H   93 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8066 (mm-30)
REVERT: H   95 GLN cc_start: 0.8108 (tt0) cc_final: 0.7145 (tm-30)
REVERT: H  105 GLU cc_start: 0.8171 (tp30) cc_final: 0.7551 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 261
  average time/residue: 0.1598
  time to fit residues: 53.1935
Evaluate side-chains
  185 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    8.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:   10.0000
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    0.1980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
A 104 HIS
B  64 ASN
D  95 GLN
E  95 GLN
G  31 HIS
G  73 ASN
** H  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.127159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.093232 restraints weight = 31022.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.096668 restraints weight = 15663.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.098974 restraints weight = 10021.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.100499 restraints weight = 7543.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.101370 restraints weight = 6339.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  12810  Z= 0.165
  Angle     :  0.633   9.518  18535  Z= 0.366
  Chirality :  0.035   0.155   2099
  Planarity :  0.005   0.071   1338
  Dihedral  : 30.149 147.544   4015
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 20.10 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.27), residues: 749
  helix:  0.31 (0.20), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.56 (0.34), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  35 
 TYR   0.017   0.002   TYR H  83 
 PHE   0.009   0.001   PHE G  25 
 TRP   0.020   0.002   TRP E  47 
 HIS   0.005   0.001   HIS E 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (12810)
  covalent geometry    : angle       0.63288 (18535)
  hydrogen bonds       : bond        0.04772 (  745)
  hydrogen bonds       : angle       3.08999 ( 1847)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 206
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.9382 (tp30) cc_final: 0.9156 (tp30)
REVERT: A   85 ASN cc_start: 0.8507 (m-40) cc_final: 0.8299 (m-40)
REVERT: B   44 LYS cc_start: 0.8560 (tttt) cc_final: 0.8004 (mmmt)
REVERT: B   45 ARG cc_start: 0.7140 (mtm180) cc_final: 0.6326 (mtt90)
REVERT: B   84 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7365 (mtm)
REVERT: C   56 GLU cc_start: 0.6606 (tt0) cc_final: 0.6316 (tt0)
REVERT: C   57 TYR cc_start: 0.8950 (t80) cc_final: 0.8343 (t80)
REVERT: C   61 GLU cc_start: 0.8709 (tp30) cc_final: 0.8304 (tp30)
REVERT: D   76 GLU cc_start: 0.8395 (tp30) cc_final: 0.8109 (tp30)
REVERT: D  106 LEU cc_start: 0.9566 (tp) cc_final: 0.9247 (tp)
REVERT: D  113 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7620 (mt-10)
REVERT: D  120 LYS cc_start: 0.8602 (ttmm) cc_final: 0.8131 (tttm)
REVERT: E   49 LYS cc_start: 0.9017 (ptmt) cc_final: 0.8394 (ptmt)
REVERT: E   73 GLU cc_start: 0.9012 (tp30) cc_final: 0.8334 (tm-30)
REVERT: E  107 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8661 (tp30)
REVERT: G   71 ARG cc_start: 0.8696 (mmm-85) cc_final: 0.7947 (ptp90)
REVERT: G   92 GLU cc_start: 0.8084 (tt0) cc_final: 0.7808 (tt0)
REVERT: H   93 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7948 (mm-30)
REVERT: H   95 GLN cc_start: 0.7956 (tt0) cc_final: 0.7035 (tm-30)
REVERT: H  105 GLU cc_start: 0.7943 (tp30) cc_final: 0.7547 (tp30)
  outliers start: 25
  outliers final: 11
  residues processed: 218
  average time/residue: 0.1315
  time to fit residues: 39.1638
Evaluate side-chains
  186 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 173
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain E residue  107 GLU
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   88 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 9 optimal weight:    8.9990
   chunk 18 optimal weight:    1.9990
   chunk 83 optimal weight:    8.9990
   chunk 85 optimal weight:   10.0000
   chunk 46 optimal weight:    3.9990
   chunk 91 optimal weight:    8.9990
   chunk 45 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0670
   chunk 3 optimal weight:   10.0000
   overall best weight:    1.7924

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
G  68 ASN
** H  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.127874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.091845 restraints weight = 33737.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.095262 restraints weight = 17029.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.097526 restraints weight = 10948.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.098984 restraints weight = 8309.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.099858 restraints weight = 7059.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12810  Z= 0.180
  Angle     :  0.627  10.371  18535  Z= 0.361
  Chirality :  0.034   0.144   2099
  Planarity :  0.005   0.059   1338
  Dihedral  : 30.028 147.195   4015
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 22.81 %
    Favored  : 72.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.29), residues: 749
  helix:  0.98 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.37 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  33 
 TYR   0.022   0.003   TYR F  88 
 PHE   0.011   0.001   PHE B 100 
 TRP   0.018   0.002   TRP E  47 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (12810)
  covalent geometry    : angle       0.62677 (18535)
  hydrogen bonds       : bond        0.04671 (  745)
  hydrogen bonds       : angle       3.01496 ( 1847)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 184
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.9381 (tp30) cc_final: 0.9169 (tp30)
REVERT: A   77 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8140 (ttpp)
REVERT: A   85 ASN cc_start: 0.8505 (m-40) cc_final: 0.8279 (m-40)
REVERT: A  110 TYR cc_start: 0.7289 (t80) cc_final: 0.7050 (t80)
REVERT: B   44 LYS cc_start: 0.8570 (tttt) cc_final: 0.8133 (mmmm)
REVERT: B   45 ARG cc_start: 0.7424 (mtm180) cc_final: 0.7064 (mtt90)
REVERT: B   84 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7108 (mtm)
REVERT: C   56 GLU cc_start: 0.6597 (tt0) cc_final: 0.6322 (tt0)
REVERT: D   59 MET cc_start: 0.8060 (tpp) cc_final: 0.7842 (tpp)
REVERT: D   79 ARG cc_start: 0.7814 (ptp90) cc_final: 0.7289 (ptp90)
REVERT: E   49 LYS cc_start: 0.9123 (ptmt) cc_final: 0.8591 (ptmt)
REVERT: E   73 GLU cc_start: 0.9085 (tp30) cc_final: 0.8359 (tm-30)
REVERT: E  107 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8751 (tp30)
REVERT: E  110 TYR cc_start: 0.6806 (t80) cc_final: 0.6599 (t80)
REVERT: F   53 GLU cc_start: 0.8218 (tt0) cc_final: 0.7922 (tt0)
REVERT: G   71 ARG cc_start: 0.8639 (mmm-85) cc_final: 0.7912 (ptp90)
REVERT: H   93 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7660 (mm-30)
REVERT: H   95 GLN cc_start: 0.8168 (tt0) cc_final: 0.7004 (tm-30)
  outliers start: 32
  outliers final: 19
  residues processed: 196
  average time/residue: 0.1226
  time to fit residues: 33.5352
Evaluate side-chains
  190 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 168
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   77 LYS
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain E residue  107 GLU
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain E residue  120 THR
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   40 TYR
Chi-restraints excluded: chain H residue   44 VAL
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue  120 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 84 optimal weight:    8.9990
   chunk 87 optimal weight:   20.0000
   chunk 20 optimal weight:    0.8980
   chunk 14 optimal weight:    8.9990
   chunk 78 optimal weight:    8.9990
   chunk 47 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 93 optimal weight:    8.9990
   chunk 41 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** C  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  68 ASN
** H  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.125580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.091947 restraints weight = 31979.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.095207 restraints weight = 16435.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.097372 restraints weight = 10613.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.098793 restraints weight = 8067.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.099665 restraints weight = 6841.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.3107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  12810  Z= 0.181
  Angle     :  0.616   9.715  18535  Z= 0.357
  Chirality :  0.034   0.153   2099
  Planarity :  0.004   0.052   1338
  Dihedral  : 29.958 146.730   4015
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 23.29 %
    Favored  : 70.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.30), residues: 749
  helix:  1.31 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -1.47 (0.35), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  92 
 TYR   0.033   0.003   TYR H  83 
 PHE   0.009   0.001   PHE B 100 
 TRP   0.018   0.002   TRP E  47 
 HIS   0.006   0.001   HIS E 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (12810)
  covalent geometry    : angle       0.61640 (18535)
  hydrogen bonds       : bond        0.04582 (  745)
  hydrogen bonds       : angle       3.01652 ( 1847)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 183
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.9337 (tp30) cc_final: 0.9135 (tp30)
REVERT: A   77 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8180 (ttpp)
REVERT: A   85 ASN cc_start: 0.8538 (m-40) cc_final: 0.8312 (m-40)
REVERT: A  110 TYR cc_start: 0.7308 (t80) cc_final: 0.6725 (t80)
REVERT: B   44 LYS cc_start: 0.8647 (tttt) cc_final: 0.8221 (pttt)
REVERT: B   45 ARG cc_start: 0.7468 (mtm180) cc_final: 0.7129 (mtt90)
REVERT: B   51 TYR cc_start: 0.7999 (m-80) cc_final: 0.7549 (m-80)
REVERT: B   84 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7250 (mtm)
REVERT: C   57 TYR cc_start: 0.8700 (t80) cc_final: 0.8185 (t80)
REVERT: C   82 HIS cc_start: 0.8204 (m-70) cc_final: 0.7966 (m-70)
REVERT: C   92 GLU cc_start: 0.8344 (mp0) cc_final: 0.7930 (pm20)
REVERT: D   79 ARG cc_start: 0.7958 (ptp90) cc_final: 0.7364 (ptp90)
REVERT: D  113 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7229 (mt-10)
REVERT: E   49 LYS cc_start: 0.9097 (ptmt) cc_final: 0.8541 (ptmt)
REVERT: E   73 GLU cc_start: 0.9062 (tp30) cc_final: 0.8370 (tm-30)
REVERT: E  107 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8738 (tp30)
REVERT: E  110 TYR cc_start: 0.6929 (t80) cc_final: 0.6643 (t80)
REVERT: F   31 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7557 (tttt)
REVERT: F   53 GLU cc_start: 0.8076 (tt0) cc_final: 0.7610 (tt0)
REVERT: G   71 ARG cc_start: 0.8675 (mmm-85) cc_final: 0.7865 (ptp-110)
REVERT: H   62 MET cc_start: 0.8915 (mmm) cc_final: 0.8711 (mmm)
REVERT: H   93 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7757 (mm-30)
REVERT: H   95 GLN cc_start: 0.8152 (tt0) cc_final: 0.7023 (tm-30)
REVERT: H  102 LEU cc_start: 0.8105 (mm) cc_final: 0.7893 (mt)
  outliers start: 36
  outliers final: 19
  residues processed: 198
  average time/residue: 0.1164
  time to fit residues: 32.3349
Evaluate side-chains
  190 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 167
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   77 LYS
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain E residue  107 GLU
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain E residue  122 PHE
Chi-restraints excluded: chain F residue   31 LYS
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   44 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 68 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0070
   chunk 56 optimal weight:    0.3980
   chunk 60 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9990
   chunk 90 optimal weight:    9.9990
   overall best weight:    0.5800

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

Flipped N/Q/H residues before XYZ refinement:
** C  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.130843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.095372 restraints weight = 33942.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.098837 restraints weight = 17125.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.101160 restraints weight = 10993.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.102677 restraints weight = 8313.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.103570 restraints weight = 7022.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.3549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  12810  Z= 0.146
  Angle     :  0.585   8.400  18535  Z= 0.338
  Chirality :  0.033   0.154   2099
  Planarity :  0.004   0.052   1338
  Dihedral  : 29.810 145.456   4015
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 27.11 %
    Favored  : 69.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.30), residues: 749
  helix:  1.50 (0.23), residues: 540
  sheet:  None (None), residues: 0
  loop : -1.30 (0.37), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  40 
 TYR   0.025   0.002   TYR D  40 
 PHE   0.007   0.001   PHE H  65 
 TRP   0.023   0.002   TRP E  47 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (12810)
  covalent geometry    : angle       0.58490 (18535)
  hydrogen bonds       : bond        0.04272 (  745)
  hydrogen bonds       : angle       2.81133 ( 1847)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 189
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.9328 (tp30) cc_final: 0.9114 (tp30)
REVERT: A   85 ASN cc_start: 0.8481 (m-40) cc_final: 0.8262 (m-40)
REVERT: B   24 ASP cc_start: 0.7772 (t0) cc_final: 0.7327 (p0)
REVERT: B   44 LYS cc_start: 0.8610 (tttt) cc_final: 0.8033 (mmmt)
REVERT: B   84 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7326 (mtm)
REVERT: C   57 TYR cc_start: 0.8611 (t80) cc_final: 0.8359 (t80)
REVERT: C   61 GLU cc_start: 0.8507 (tp30) cc_final: 0.8020 (tp30)
REVERT: C   65 LEU cc_start: 0.9408 (mp) cc_final: 0.9108 (mp)
REVERT: C   92 GLU cc_start: 0.8303 (mp0) cc_final: 0.7946 (pm20)
REVERT: D   79 ARG cc_start: 0.7937 (ptp90) cc_final: 0.7339 (ptp90)
REVERT: E   49 LYS cc_start: 0.9054 (ptmt) cc_final: 0.8433 (ptmt)
REVERT: E   73 GLU cc_start: 0.9026 (tp30) cc_final: 0.8274 (tp30)
REVERT: E  110 TYR cc_start: 0.6769 (t80) cc_final: 0.6520 (t80)
REVERT: F   31 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7494 (tttt)
REVERT: F   53 GLU cc_start: 0.8172 (tt0) cc_final: 0.7746 (tt0)
REVERT: F   79 LYS cc_start: 0.7458 (mtpp) cc_final: 0.7102 (ttpp)
REVERT: G   71 ARG cc_start: 0.8648 (mmm-85) cc_final: 0.7885 (ptp-110)
REVERT: H   62 MET cc_start: 0.8919 (mmm) cc_final: 0.8713 (mmm)
REVERT: H   93 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7789 (mm-30)
REVERT: H   95 GLN cc_start: 0.8019 (tt0) cc_final: 0.6956 (tm-30)
  outliers start: 21
  outliers final: 10
  residues processed: 196
  average time/residue: 0.1200
  time to fit residues: 32.7961
Evaluate side-chains
  183 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 171
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain E residue  122 PHE
Chi-restraints excluded: chain F residue   31 LYS
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  111 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 92 optimal weight:    8.9990
   chunk 47 optimal weight:    0.5980
   chunk 30 optimal weight:    6.9990
   chunk 57 optimal weight:    0.0270
   chunk 2 optimal weight:    0.9990
   chunk 73 optimal weight:   20.0000
   chunk 15 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0010
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.4644

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

Flipped N/Q/H residues before XYZ refinement:
C  31 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.132363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.097141 restraints weight = 34104.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.100642 restraints weight = 17306.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.102975 restraints weight = 11093.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.104556 restraints weight = 8356.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.105549 restraints weight = 7004.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.3925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12810  Z= 0.144
  Angle     :  0.581   8.270  18535  Z= 0.335
  Chirality :  0.032   0.164   2099
  Planarity :  0.004   0.056   1338
  Dihedral  : 29.759 144.828   4015
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 28.55 %
    Favored  : 68.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.30), residues: 749
  helix:  1.52 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -1.17 (0.38), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  40 
 TYR   0.040   0.002   TYR H  83 
 PHE   0.013   0.001   PHE F 100 
 TRP   0.026   0.002   TRP E  47 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (12810)
  covalent geometry    : angle       0.58131 (18535)
  hydrogen bonds       : bond        0.04225 (  745)
  hydrogen bonds       : angle       2.77652 ( 1847)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 192
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.9341 (tp30) cc_final: 0.9117 (tp30)
REVERT: A   95 GLN cc_start: 0.7612 (tp40) cc_final: 0.7263 (tp40)
REVERT: A  128 LEU cc_start: 0.8448 (tt) cc_final: 0.8242 (tp)
REVERT: B   24 ASP cc_start: 0.7704 (t0) cc_final: 0.7328 (p0)
REVERT: B   29 ILE cc_start: 0.7817 (mm) cc_final: 0.7486 (mp)
REVERT: B   44 LYS cc_start: 0.8497 (tttt) cc_final: 0.8080 (mmmt)
REVERT: B   45 ARG cc_start: 0.6657 (mtt180) cc_final: 0.6428 (ttm170)
REVERT: B   84 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7200 (mtm)
REVERT: C   57 TYR cc_start: 0.8608 (t80) cc_final: 0.8342 (t80)
REVERT: C   61 GLU cc_start: 0.8540 (tp30) cc_final: 0.7990 (tp30)
REVERT: C   65 LEU cc_start: 0.9422 (mp) cc_final: 0.9083 (mp)
REVERT: C   92 GLU cc_start: 0.8236 (mp0) cc_final: 0.7910 (pm20)
REVERT: D   42 TYR cc_start: 0.6468 (OUTLIER) cc_final: 0.6231 (t80)
REVERT: D   79 ARG cc_start: 0.7931 (ptp90) cc_final: 0.7348 (ptp90)
REVERT: D   85 LYS cc_start: 0.8705 (mmmt) cc_final: 0.8453 (tppt)
REVERT: E   49 LYS cc_start: 0.9033 (ptmt) cc_final: 0.8552 (ptmt)
REVERT: E   73 GLU cc_start: 0.9023 (tp30) cc_final: 0.8240 (tp30)
REVERT: E  110 TYR cc_start: 0.6786 (t80) cc_final: 0.6512 (t80)
REVERT: F   31 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7474 (tttt)
REVERT: F   53 GLU cc_start: 0.8162 (tt0) cc_final: 0.7717 (tt0)
REVERT: F   79 LYS cc_start: 0.7393 (mtpp) cc_final: 0.7013 (ttpp)
REVERT: F   84 MET cc_start: 0.7362 (mmp) cc_final: 0.6865 (mmp)
REVERT: G   71 ARG cc_start: 0.8631 (mmm-85) cc_final: 0.7835 (ptp90)
REVERT: G   78 ILE cc_start: 0.7814 (mt) cc_final: 0.7537 (mm)
REVERT: H   62 MET cc_start: 0.8932 (mmm) cc_final: 0.8721 (mmm)
REVERT: H   93 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7730 (mm-30)
REVERT: H   95 GLN cc_start: 0.8013 (tt0) cc_final: 0.7028 (tm-30)
  outliers start: 21
  outliers final: 16
  residues processed: 201
  average time/residue: 0.1205
  time to fit residues: 33.9127
Evaluate side-chains
  193 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 174
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   42 TYR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain F residue   31 LYS
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  111 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 85 optimal weight:   10.0000
   chunk 8 optimal weight:    0.8980
   chunk 83 optimal weight:    7.9990
   chunk 15 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** B  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.128005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.094855 restraints weight = 32175.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.098021 restraints weight = 16893.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.100167 restraints weight = 11023.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.101584 restraints weight = 8390.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.102398 restraints weight = 7107.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.4028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  12810  Z= 0.165
  Angle     :  0.598   7.579  18535  Z= 0.343
  Chirality :  0.033   0.161   2099
  Planarity :  0.004   0.052   1338
  Dihedral  : 29.915 145.240   4015
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 29.51 %
    Favored  : 66.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.30), residues: 749
  helix:  1.50 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -1.17 (0.38), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG D  86 
 TYR   0.059   0.003   TYR H  83 
 PHE   0.007   0.001   PHE F 100 
 TRP   0.026   0.002   TRP E  47 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (12810)
  covalent geometry    : angle       0.59843 (18535)
  hydrogen bonds       : bond        0.04356 (  745)
  hydrogen bonds       : angle       2.91394 ( 1847)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 175
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.9368 (tp30) cc_final: 0.9158 (tp30)
REVERT: B   24 ASP cc_start: 0.7823 (t0) cc_final: 0.7397 (p0)
REVERT: B   29 ILE cc_start: 0.7926 (mm) cc_final: 0.7604 (mp)
REVERT: B   44 LYS cc_start: 0.8545 (tttt) cc_final: 0.8312 (pttt)
REVERT: B   45 ARG cc_start: 0.6417 (mtt180) cc_final: 0.5782 (ttm170)
REVERT: B   84 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7139 (mtm)
REVERT: C   61 GLU cc_start: 0.8580 (tp30) cc_final: 0.8235 (tp30)
REVERT: C   65 LEU cc_start: 0.9446 (mp) cc_final: 0.9154 (mp)
REVERT: D   42 TYR cc_start: 0.6602 (OUTLIER) cc_final: 0.6340 (t80)
REVERT: D   48 VAL cc_start: 0.8349 (OUTLIER) cc_final: 0.8123 (p)
REVERT: D   79 ARG cc_start: 0.7986 (ptp90) cc_final: 0.7145 (ptp90)
REVERT: E   49 LYS cc_start: 0.9061 (ptmt) cc_final: 0.8633 (ptmt)
REVERT: E   73 GLU cc_start: 0.9057 (tp30) cc_final: 0.8209 (tm-30)
REVERT: E  110 TYR cc_start: 0.6918 (t80) cc_final: 0.6619 (t80)
REVERT: F   31 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7501 (tttt)
REVERT: F   53 GLU cc_start: 0.8093 (tt0) cc_final: 0.7696 (tt0)
REVERT: F   93 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8202 (tt0)
REVERT: G   71 ARG cc_start: 0.8643 (mmm-85) cc_final: 0.7808 (ptp-110)
REVERT: H   62 MET cc_start: 0.9006 (mmm) cc_final: 0.8777 (mmm)
REVERT: H   93 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7677 (mm-30)
REVERT: H   95 GLN cc_start: 0.8039 (tt0) cc_final: 0.6978 (tm-30)
  outliers start: 28
  outliers final: 16
  residues processed: 188
  average time/residue: 0.1222
  time to fit residues: 32.4592
Evaluate side-chains
  186 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 165
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   42 TYR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain F residue   31 LYS
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   94 ASN
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  111 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 72 optimal weight:    3.9990
   chunk 9 optimal weight:    8.9990
   chunk 75 optimal weight:    8.9990
   chunk 43 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    7.9990
   chunk 71 optimal weight:    3.9990
   chunk 84 optimal weight:   10.0000
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
G  68 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.121346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.087617 restraints weight = 32772.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.090577 restraints weight = 17281.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.092536 restraints weight = 11400.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.093782 restraints weight = 8812.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.094555 restraints weight = 7564.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.3929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  12810  Z= 0.274
  Angle     :  0.713  12.762  18535  Z= 0.405
  Chirality :  0.038   0.165   2099
  Planarity :  0.005   0.047   1338
  Dihedral  : 30.451 146.580   4015
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 29.51 %
    Favored  : 65.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.29), residues: 749
  helix:  0.94 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.36 (0.35), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  86 
 TYR   0.083   0.004   TYR H  83 
 PHE   0.018   0.002   PHE A  84 
 TRP   0.019   0.002   TRP E  47 
 HIS   0.007   0.002   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00605 (12810)
  covalent geometry    : angle       0.71331 (18535)
  hydrogen bonds       : bond        0.05509 (  745)
  hydrogen bonds       : angle       3.54249 ( 1847)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 168
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 TYR cc_start: 0.7786 (t80) cc_final: 0.7488 (t80)
REVERT: B   24 ASP cc_start: 0.8052 (t0) cc_final: 0.7639 (p0)
REVERT: B   44 LYS cc_start: 0.8516 (tttt) cc_final: 0.8157 (mmmt)
REVERT: B   51 TYR cc_start: 0.8152 (m-80) cc_final: 0.7777 (m-80)
REVERT: B   59 LYS cc_start: 0.8302 (tppt) cc_final: 0.8053 (tppt)
REVERT: B   84 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7084 (mtm)
REVERT: C   77 ARG cc_start: 0.7187 (ttm-80) cc_final: 0.6903 (mtt-85)
REVERT: C   92 GLU cc_start: 0.8377 (mp0) cc_final: 0.7997 (pm20)
REVERT: D   59 MET cc_start: 0.8082 (tpp) cc_final: 0.7722 (tpp)
REVERT: D   93 GLU cc_start: 0.8359 (mp0) cc_final: 0.7884 (mm-30)
REVERT: E   49 LYS cc_start: 0.9054 (ptmt) cc_final: 0.8525 (ptmt)
REVERT: E   73 GLU cc_start: 0.9109 (tp30) cc_final: 0.8322 (tm-30)
REVERT: E  110 TYR cc_start: 0.7473 (t80) cc_final: 0.7109 (t80)
REVERT: F   31 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7587 (tttm)
REVERT: F   53 GLU cc_start: 0.7966 (tt0) cc_final: 0.7591 (tt0)
REVERT: F   59 LYS cc_start: 0.8814 (tttt) cc_final: 0.8410 (tmtt)
REVERT: G   71 ARG cc_start: 0.8698 (mmm-85) cc_final: 0.7804 (ptp-170)
REVERT: G   95 LYS cc_start: 0.8538 (ttmt) cc_final: 0.8312 (ttmm)
REVERT: H   62 MET cc_start: 0.9071 (mmm) cc_final: 0.8829 (mmm)
REVERT: H   93 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7709 (mm-30)
  outliers start: 34
  outliers final: 19
  residues processed: 182
  average time/residue: 0.1175
  time to fit residues: 30.1015
Evaluate side-chains
  182 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 161
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain F residue   31 LYS
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue   94 ASN
Chi-restraints excluded: chain G residue  111 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 97 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9980
   chunk 74 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 79 optimal weight:    7.9990
   chunk 26 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 95 optimal weight:    6.9990
   chunk 89 optimal weight:   10.0000
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
** B  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  64 ASN
G  68 ASN
G  84 GLN
** H  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.127146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.091399 restraints weight = 34243.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.094697 restraints weight = 17645.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.096869 restraints weight = 11437.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.098285 restraints weight = 8730.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.099107 restraints weight = 7426.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.4116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12810  Z= 0.183
  Angle     :  0.649   9.198  18535  Z= 0.367
  Chirality :  0.035   0.178   2099
  Planarity :  0.004   0.049   1338
  Dihedral  : 30.249 145.807   4015
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 30.78 %
    Favored  : 65.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.29), residues: 749
  helix:  1.10 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -1.40 (0.35), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  86 
 TYR   0.064   0.003   TYR H  83 
 PHE   0.009   0.001   PHE F 100 
 TRP   0.025   0.002   TRP E  47 
 HIS   0.006   0.001   HIS E 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 (12810)
  covalent geometry    : angle       0.64938 (18535)
  hydrogen bonds       : bond        0.04598 (  745)
  hydrogen bonds       : angle       3.21346 ( 1847)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 169
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 ASP cc_start: 0.8099 (t0) cc_final: 0.7580 (p0)
REVERT: B   29 ILE cc_start: 0.7966 (mm) cc_final: 0.7634 (mp)
REVERT: B   44 LYS cc_start: 0.8547 (tttt) cc_final: 0.8329 (pttt)
REVERT: B   51 TYR cc_start: 0.8063 (m-80) cc_final: 0.7651 (m-80)
REVERT: B   84 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7054 (mtm)
REVERT: C   57 TYR cc_start: 0.8386 (t80) cc_final: 0.8021 (t80)
REVERT: C   92 GLU cc_start: 0.8308 (mp0) cc_final: 0.7894 (pm20)
REVERT: D   93 GLU cc_start: 0.8232 (mp0) cc_final: 0.7760 (mm-30)
REVERT: E   49 LYS cc_start: 0.9024 (ptmt) cc_final: 0.8788 (ptmt)
REVERT: E   73 GLU cc_start: 0.9101 (tp30) cc_final: 0.8304 (tm-30)
REVERT: E  110 TYR cc_start: 0.7121 (t80) cc_final: 0.6810 (t80)
REVERT: F   31 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7502 (tttt)
REVERT: F   53 GLU cc_start: 0.8045 (tt0) cc_final: 0.7781 (tt0)
REVERT: F   59 LYS cc_start: 0.8788 (tttt) cc_final: 0.8370 (tmtt)
REVERT: F   93 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8099 (tt0)
REVERT: G   71 ARG cc_start: 0.8678 (mmm-85) cc_final: 0.7785 (ptp-170)
REVERT: G   95 LYS cc_start: 0.8490 (ttmt) cc_final: 0.8266 (ttmm)
REVERT: H   93 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7792 (mm-30)
REVERT: H   95 GLN cc_start: 0.8181 (tt0) cc_final: 0.7336 (tm-30)
  outliers start: 23
  outliers final: 16
  residues processed: 180
  average time/residue: 0.1069
  time to fit residues: 27.4840
Evaluate side-chains
  182 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 163
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain F residue   31 LYS
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   94 ASN
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue  102 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 38 optimal weight:    0.0570
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 85 optimal weight:   10.0000
   chunk 2 optimal weight:    0.0670
   chunk 44 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9990
   overall best weight:    1.4242

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

Flipped N/Q/H residues before XYZ refinement:
** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  68 ASN
** H  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.126141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.093111 restraints weight = 32583.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.096253 restraints weight = 16852.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.098374 restraints weight = 10934.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.099729 restraints weight = 8325.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.100564 restraints weight = 7067.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.4258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12810  Z= 0.168
  Angle     :  0.642   9.354  18535  Z= 0.361
  Chirality :  0.034   0.169   2099
  Planarity :  0.004   0.050   1338
  Dihedral  : 30.150 145.375   4015
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 32.22 %
    Favored  : 65.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.30), residues: 749
  helix:  1.18 (0.22), residues: 539
  sheet:  None (None), residues: 0
  loop : -1.31 (0.35), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  86 
 TYR   0.059   0.003   TYR H  83 
 PHE   0.009   0.001   PHE F 100 
 TRP   0.025   0.002   TRP E  47 
 HIS   0.006   0.001   HIS E 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (12810)
  covalent geometry    : angle       0.64183 (18535)
  hydrogen bonds       : bond        0.04491 (  745)
  hydrogen bonds       : angle       3.10265 ( 1847)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 167
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 ASP cc_start: 0.8003 (t0) cc_final: 0.7574 (p0)
REVERT: B   51 TYR cc_start: 0.8023 (m-80) cc_final: 0.7586 (m-80)
REVERT: B   84 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7093 (mtm)
REVERT: C   92 GLU cc_start: 0.8376 (mp0) cc_final: 0.7974 (pm20)
REVERT: D   93 GLU cc_start: 0.8204 (mp0) cc_final: 0.7732 (mm-30)
REVERT: E   49 LYS cc_start: 0.9009 (ptmt) cc_final: 0.8768 (ptmt)
REVERT: E   73 GLU cc_start: 0.9058 (tp30) cc_final: 0.8229 (tm-30)
REVERT: E  110 TYR cc_start: 0.7070 (t80) cc_final: 0.6739 (t80)
REVERT: F   53 GLU cc_start: 0.8084 (tt0) cc_final: 0.7840 (tt0)
REVERT: F   59 LYS cc_start: 0.8763 (tttt) cc_final: 0.8333 (tmtt)
REVERT: F   84 MET cc_start: 0.7277 (mmp) cc_final: 0.7015 (mmp)
REVERT: F   93 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7908 (tt0)
REVERT: G   71 ARG cc_start: 0.8637 (mmm-85) cc_final: 0.8239 (ttm110)
REVERT: G   95 LYS cc_start: 0.8496 (ttmt) cc_final: 0.8272 (ttmm)
REVERT: H   93 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7706 (mm-30)
REVERT: H   95 GLN cc_start: 0.8142 (tt0) cc_final: 0.7342 (tm-30)
  outliers start: 16
  outliers final: 13
  residues processed: 174
  average time/residue: 0.1075
  time to fit residues: 26.9422
Evaluate side-chains
  178 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 163
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue  102 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 88 optimal weight:   10.0000
   chunk 69 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 26 optimal weight:    9.9990
   chunk 1 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 80 optimal weight:    8.9990
   chunk 43 optimal weight:    0.9990
   chunk 83 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  68 ASN
** H  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.127869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.092030 restraints weight = 34542.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.095268 restraints weight = 17834.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.097449 restraints weight = 11585.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.098854 restraints weight = 8825.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.099682 restraints weight = 7498.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.4300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12810  Z= 0.185
  Angle     :  0.651  10.593  18535  Z= 0.367
  Chirality :  0.035   0.173   2099
  Planarity :  0.004   0.049   1338
  Dihedral  : 30.158 145.708   4015
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 31.42 %
    Favored  : 64.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.29), residues: 749
  helix:  1.16 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.29 (0.34), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  86 
 TYR   0.060   0.003   TYR H  83 
 PHE   0.009   0.001   PHE G  25 
 TRP   0.023   0.002   TRP E  47 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (12810)
  covalent geometry    : angle       0.65073 (18535)
  hydrogen bonds       : bond        0.04604 (  745)
  hydrogen bonds       : angle       3.18984 ( 1847)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2081.93 seconds
wall clock time: 36 minutes 33.88 seconds (2193.88 seconds total)