Starting phenix.real_space_refine
on Sun Apr  5 16:28:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y7i_33666/04_2026/7y7i_33666.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y7i_33666/04_2026/7y7i_33666.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.42
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y7i_33666/04_2026/7y7i_33666.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y7i_33666/04_2026/7y7i_33666.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y7i_33666/04_2026/7y7i_33666.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y7i_33666/04_2026/7y7i_33666.map"
  }
  resolution = 3.42
  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=   0.001 sd=   0.010
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     286      5.49       5
     S      14      5.16       5
     C    6943      2.51       5
     N    2341      2.21       5
     O    2861      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12445
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 845
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 3, 'TRANS': 98}
    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: 826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 826
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 740
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 811
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 619
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 810
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 2915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 2915
          Classifications: {'DNA': 143}
          Link IDs: {'rna3p': 142}
    Chain: "J"
      Number of atoms: 2948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 2948
          Classifications: {'DNA': 143}
          Link IDs: {'rna3p': 142}
    Chain: "K"
      Number of atoms: 281
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 281
          Classifications: {'peptide': 34}
          Link IDs: {'PTRANS': 2, 'TRANS': 31}
    Chain: "L"
      Number of atoms: 281
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 281
          Classifications: {'peptide': 34}
          Link IDs: {'PTRANS': 2, 'TRANS': 31}
  Time building chain proxies: 2.87, per 1000 atoms: 0.23
  Number of scatterers: 12445
  At special positions: 0
  Unit cell: (117.6, 111.72, 116.62, 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      14     16.00
     P     286     15.00
     O    2861      8.00
     N    2341      7.00
     C    6943      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: 0.73
  Conformation dependent library (CDL) restraints added in 238.5 milliseconds
  

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1528

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 12 sheets defined
      67.8% alpha, 3.6% beta
      136 base pairs and 228 stacking pairs defined.
    Time for finding SS restraints: 1.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
      removed outlier: 4.057A  pdb=" N   ARG A  49 " --> pdb=" O   THR A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 80
    Processing helix  chain 'A' and resid 87 through 116
      removed outlier: 3.684A  pdb=" N   LEU A  91 " --> pdb=" O   GLN A  87 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LEU A  92 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 133
      removed outlier: 3.629A  pdb=" N   LEU A 126 " --> pdb=" O   TYR A 122 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ARG A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 139
      removed outlier: 3.901A  pdb=" N   GLY A 139 " --> pdb=" O   LEU A 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.684A  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: 4.058A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.694A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 23
    Processing helix  chain 'C' and resid 28 through 38
    Processing helix  chain 'C' and resid 47 through 74
    Processing helix  chain 'C' and resid 80 through 90
      removed outlier: 3.607A  pdb=" N   ASN C  90 " --> pdb=" O   LEU C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 98
      removed outlier: 3.987A  pdb=" N   LYS C  96 " --> pdb=" O   GLU C  92 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.707A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.558A  pdb=" N   MET D  59 " --> pdb=" O   SER D  55 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.553A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 123
      removed outlier: 3.691A  pdb=" N   SER D 123 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.978A  pdb=" N   ARG E  49 " --> pdb=" O   THR E  45 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   SER E  57 " --> pdb=" O   ARG E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 80
      removed outlier: 3.546A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 116
      removed outlier: 3.694A  pdb=" N   LEU E  91 " --> pdb=" O   GLN E  87 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LEU E  92 " --> pdb=" O   ALA E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 133
      removed outlier: 3.794A  pdb=" N   LEU E 126 " --> pdb=" O   TYR E 122 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
      removed outlier: 3.615A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.812A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.504A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 22
      removed outlier: 3.836A  pdb=" N   ALA G  22 " --> pdb=" O   ARG G  18 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 28 through 38
    Processing helix  chain 'G' and resid 46 through 74
      removed outlier: 4.410A  pdb=" N   VAL G  50 " --> pdb=" O   ALA G  46 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 80 through 89
    Processing helix  chain 'G' and resid 91 through 98
      removed outlier: 4.103A  pdb=" N   LEU G  97 " --> pdb=" O   GLU G  93 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 38 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.605A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.793A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 104 through 123
    Processing helix  chain 'K' and resid 534 through 538
    Processing helix  chain 'L' and resid 534 through 538
    Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86
      removed outlier: 6.594A  pdb=" N   ARG 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 'B' and resid 96 through 98
      removed outlier: 6.559A  pdb=" N   THR B  96 " --> pdb=" O   THR G 102 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44
      removed outlier: 7.636A  pdb=" N   ARG C  43 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79
      removed outlier: 3.560A  pdb=" N   ILE C  79 " --> pdb=" O   GLY D  53 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 86
      removed outlier: 6.818A  pdb=" N   ARG E  85 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 120 through 121
    Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44
      removed outlier: 7.584A  pdb=" N   ARG G  43 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79
    Processing sheet with id=AB2, first strand: chain 'K' and resid 541 through 543
    Processing sheet with id=AB3, first strand: chain 'L' and resid 540 through 542

    393 hydrogen bonds defined for protein.
    1152 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      351 hydrogen bonds
      702 hydrogen bond angles
      0 basepair planarities
      136 basepair parallelities
      228 stacking parallelities
  Total time for adding SS restraints: 2.42

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2513
        1.33 -     1.45: 4151
        1.45 -     1.57: 6002
        1.57 -     1.69: 570
        1.69 -     1.81: 22
  Bond restraints: 13258
  Sorted by residual:
  bond pdb=" CB  MET H  59 "
       pdb=" CG  MET H  59 "
    ideal  model  delta    sigma   weight residual
    1.520  1.482  0.038 3.00e-02 1.11e+03 1.62e+00
  bond pdb=" C3'  DC J 192 "
       pdb=" O3'  DC J 192 "
    ideal  model  delta    sigma   weight residual
    1.422  1.460 -0.038 3.00e-02 1.11e+03 1.59e+00
  bond pdb=" C3'  DC J 178 "
       pdb=" O3'  DC J 178 "
    ideal  model  delta    sigma   weight residual
    1.422  1.459 -0.037 3.00e-02 1.11e+03 1.50e+00
  bond pdb=" C1'  DT I 103 "
       pdb=" N1   DT I 103 "
    ideal  model  delta    sigma   weight residual
    1.490  1.525 -0.035 3.00e-02 1.11e+03 1.37e+00
  bond pdb=" C3'  DC J 242 "
       pdb=" C2'  DC J 242 "
    ideal  model  delta    sigma   weight residual
    1.525  1.546 -0.021 2.00e-02 2.50e+03 1.09e+00
  ... (remaining 13253 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 18584
        1.58 -     3.15: 510
        3.15 -     4.73: 32
        4.73 -     6.30: 7
        6.30 -     7.88: 2
  Bond angle restraints: 19135
  Sorted by residual:
  angle pdb=" C3'  DC J 190 "
        pdb=" C2'  DC J 190 "
        pdb=" C1'  DC J 190 "
      ideal   model   delta    sigma   weight residual
     101.60   96.94    4.66 1.50e+00 4.44e-01 9.65e+00
  angle pdb=" CB  MET H  59 "
        pdb=" CG  MET H  59 "
        pdb=" SD  MET H  59 "
      ideal   model   delta    sigma   weight residual
     112.70  104.82    7.88 3.00e+00 1.11e-01 6.90e+00
  angle pdb=" C   ASN G 111 "
        pdb=" CA  ASN G 111 "
        pdb=" CB  ASN G 111 "
      ideal   model   delta    sigma   weight residual
     109.68  114.86   -5.18 1.98e+00 2.55e-01 6.84e+00
  angle pdb=" C3'  DC J 192 "
        pdb=" O3'  DC J 192 "
        pdb=" P    DC J 193 "
      ideal   model   delta    sigma   weight residual
     120.20  123.84   -3.64 1.50e+00 4.44e-01 5.89e+00
  angle pdb=" C4'  DG I  66 "
        pdb=" C3'  DG I  66 "
        pdb=" C2'  DG I  66 "
      ideal   model   delta    sigma   weight residual
     102.40   98.79    3.61 1.50e+00 4.44e-01 5.81e+00
  ... (remaining 19130 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.68: 5122
       25.68 -    51.37: 1590
       51.37 -    77.05: 472
       77.05 -   102.73: 26
      102.73 -   128.41: 2
  Dihedral angle restraints: 7212
    sinusoidal: 4834
      harmonic: 2378
  Sorted by residual:
  dihedral pdb=" C4'  DC J 178 "
           pdb=" C3'  DC J 178 "
           pdb=" O3'  DC J 178 "
           pdb=" P    DT J 179 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00  -11.59 -128.41     1      3.50e+01 8.16e-04 1.27e+01
  dihedral pdb=" C4'  DC J 192 "
           pdb=" C3'  DC J 192 "
           pdb=" O3'  DC J 192 "
           pdb=" P    DC J 193 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00  -13.98 -126.02     1      3.50e+01 8.16e-04 1.24e+01
  dihedral pdb=" CA  ARG E  80 "
           pdb=" C   ARG E  80 "
           pdb=" N   GLY E  81 "
           pdb=" CA  GLY E  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.25   16.75     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 7209 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1519
       0.032 -    0.064: 478
       0.064 -    0.095: 117
       0.095 -    0.127: 46
       0.127 -    0.159: 5
  Chirality restraints: 2165
  Sorted by residual:
  chirality pdb=" C3'  DC J 191 "
            pdb=" C4'  DC J 191 "
            pdb=" O3'  DC J 191 "
            pdb=" C2'  DC J 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.82    0.16 2.00e-01 2.50e+01 6.32e-01
  chirality pdb=" C3'  DC J 190 "
            pdb=" C4'  DC J 190 "
            pdb=" O3'  DC J 190 "
            pdb=" C2'  DC J 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.82    0.16 2.00e-01 2.50e+01 6.24e-01
  chirality pdb=" CA  ILE G 112 "
            pdb=" N   ILE G 112 "
            pdb=" C   ILE G 112 "
            pdb=" CB  ILE G 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.44e-01
  ... (remaining 2162 not shown)

  Planarity restraints: 1429
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J 162 "   -0.016 2.00e-02 2.50e+03   1.52e-02 6.92e+00
        pdb=" N9   DG J 162 "    0.022 2.00e-02 2.50e+03
        pdb=" C8   DG J 162 "    0.001 2.00e-02 2.50e+03
        pdb=" N7   DG J 162 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DG J 162 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DG J 162 "   -0.013 2.00e-02 2.50e+03
        pdb=" O6   DG J 162 "    0.004 2.00e-02 2.50e+03
        pdb=" N1   DG J 162 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DG J 162 "   -0.034 2.00e-02 2.50e+03
        pdb=" N2   DG J 162 "    0.026 2.00e-02 2.50e+03
        pdb=" N3   DG J 162 "    0.001 2.00e-02 2.50e+03
        pdb=" C4   DG J 162 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS K 530 "   -0.039 5.00e-02 4.00e+02   5.95e-02 5.67e+00
        pdb=" N   PRO K 531 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO K 531 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO K 531 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I  63 "   -0.006 2.00e-02 2.50e+03   1.30e-02 3.80e+00
        pdb=" N1   DC I  63 "    0.008 2.00e-02 2.50e+03
        pdb=" C2   DC I  63 "   -0.031 2.00e-02 2.50e+03
        pdb=" O2   DC I  63 "    0.021 2.00e-02 2.50e+03
        pdb=" N3   DC I  63 "    0.001 2.00e-02 2.50e+03
        pdb=" C4   DC I  63 "   -0.003 2.00e-02 2.50e+03
        pdb=" N4   DC I  63 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DC I  63 "    0.004 2.00e-02 2.50e+03
        pdb=" C6   DC I  63 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1426 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1936
        2.77 -     3.30: 11063
        3.30 -     3.83: 23605
        3.83 -     4.37: 26505
        4.37 -     4.90: 40152
  Nonbonded interactions: 103261
  Sorted by model distance:
  nonbonded pdb=" OG1 THR L 523 "
            pdb=" OG  SER L 525 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" NH2 ARG A  40 "
            pdb=" O2   DT J 227 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" O   TYR C  40 "
            pdb=" OG  SER D  78 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OH  TYR C  40 "
            pdb=" OE1 GLU D  71 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" N2   DG I 127 "
            pdb=" N3   DC J 164 "
     model   vdw
     2.305 3.200
  ... (remaining 103256 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 38 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 25 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 14 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 31 through 123)
  selection = chain 'H'
}
ncs_group {
  reference = chain 'K'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.450
  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:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     12.700
  Find NCS groups from input model:        0.140
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
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      :  0.004   0.038  13258  Z= 0.161
  Angle     :  0.571   7.878  19135  Z= 0.342
  Chirality :  0.036   0.159   2165
  Planarity :  0.004   0.060   1429
  Dihedral  : 28.764 128.413   5684
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  : 14.85 %
    Favored  : 85.01 %
  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 are not related in a simple way.
  whole:  2.18 (0.30), residues: 804
  helix:  2.59 (0.23), residues: 511
  sheet: -2.85 (0.88), residues: 26
  loop : -0.40 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  86 
 TYR   0.031   0.001   TYR B  88 
 PHE   0.006   0.001   PHE E  78 
 TRP   0.008   0.001   TRP K 536 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (13258)
  covalent geometry    : angle       0.57069 (19135)
  hydrogen bonds       : bond        0.10507 (  744)
  hydrogen bonds       : angle       3.77518 ( 1854)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 159
  time to evaluate  : 0.274 
Fit side-chains
REVERT: B   91 LYS cc_start: 0.8317 (tttt) cc_final: 0.7879 (tmtt)
REVERT: C   21 ARG cc_start: 0.8186 (mmm-85) cc_final: 0.7973 (mmm-85)
REVERT: C   96 LYS cc_start: 0.8211 (mtpp) cc_final: 0.7839 (mtmm)
REVERT: D   99 ARG cc_start: 0.8696 (mmm-85) cc_final: 0.8070 (mtm-85)
REVERT: D  119 THR cc_start: 0.8233 (m) cc_final: 0.7866 (p)
REVERT: E   42 ARG cc_start: 0.7621 (mtm180) cc_final: 0.7364 (mtp180)
REVERT: E   77 LEU cc_start: 0.8318 (tt) cc_final: 0.8055 (tp)
REVERT: E   89 MET cc_start: 0.7559 (mmm) cc_final: 0.7159 (mmt)
REVERT: F   29 ILE cc_start: 0.8516 (mp) cc_final: 0.8231 (mm)
REVERT: F   79 LYS cc_start: 0.8403 (mttp) cc_final: 0.8168 (mmtp)
REVERT: H   34 LYS cc_start: 0.7799 (tptt) cc_final: 0.6514 (mttt)
REVERT: L  544 ASP cc_start: 0.7010 (p0) cc_final: 0.6722 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 160
  average time/residue: 0.2316
  time to fit residues: 45.1865
Evaluate side-chains
  98 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    9.9990
   chunk 100 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    3.4786

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
C  25 GLN
H  49 HIS
K 548 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.173957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.137820 restraints weight = 14958.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 0.94
r_work: 0.3065 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  13258  Z= 0.250
  Angle     :  0.681   9.426  19135  Z= 0.400
  Chirality :  0.043   0.205   2165
  Planarity :  0.006   0.073   1429
  Dihedral  : 31.750 126.356   4056
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 13.68 %
    Favored  : 83.84 %
  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 are not related in a simple way.
  whole:  1.97 (0.29), residues: 804
  helix:  2.25 (0.22), residues: 529
  sheet:  None (None), residues: 0
  loop : -0.58 (0.35), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E  80 
 TYR   0.039   0.002   TYR B  88 
 PHE   0.020   0.002   PHE K 535 
 TRP   0.006   0.002   TRP K 536 
 HIS   0.005   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00576 (13258)
  covalent geometry    : angle       0.68127 (19135)
  hydrogen bonds       : bond        0.06960 (  744)
  hydrogen bonds       : angle       3.18426 ( 1854)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.348 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8459 (mt)
REVERT: A  111 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8373 (mp)
REVERT: B   91 LYS cc_start: 0.8436 (tttt) cc_final: 0.7929 (ttpp)
REVERT: C   65 GLU cc_start: 0.8592 (tt0) cc_final: 0.8268 (tt0)
REVERT: D   99 ARG cc_start: 0.8754 (mmm-85) cc_final: 0.8216 (mtm-85)
REVERT: D  119 THR cc_start: 0.8575 (m) cc_final: 0.8196 (p)
REVERT: E   48 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8800 (mm)
REVERT: E   89 MET cc_start: 0.7919 (mmm) cc_final: 0.7363 (mmt)
REVERT: E  108 ASP cc_start: 0.8198 (m-30) cc_final: 0.7985 (m-30)
REVERT: G   65 GLU cc_start: 0.8279 (tp30) cc_final: 0.7762 (tt0)
REVERT: H   34 LYS cc_start: 0.7500 (tptt) cc_final: 0.6510 (mttt)
REVERT: K  521 ILE cc_start: 0.3179 (OUTLIER) cc_final: 0.2701 (mm)
REVERT: L  523 THR cc_start: 0.8005 (p) cc_final: 0.7774 (p)
  outliers start: 17
  outliers final: 7
  residues processed: 115
  average time/residue: 0.1777
  time to fit residues: 26.3923
Evaluate side-chains
  99 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain K residue  521 ILE
Chi-restraints excluded: chain L residue  533 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 104 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   chunk 87 optimal weight:    8.9990
   chunk 21 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 79 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 80 optimal weight:   10.0000
   overall best weight:    1.9988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.175071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.137900 restraints weight = 15183.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 0.90
r_work: 0.3135 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13258  Z= 0.182
  Angle     :  0.588   6.731  19135  Z= 0.352
  Chirality :  0.038   0.171   2165
  Planarity :  0.004   0.054   1429
  Dihedral  : 31.398 123.184   4056
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.99 %
    Favored  : 82.82 %
  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 are not related in a simple way.
  whole:  2.24 (0.30), residues: 804
  helix:  2.60 (0.22), residues: 521
  sheet: -2.30 (1.29), residues: 20
  loop : -0.54 (0.35), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E  80 
 TYR   0.025   0.001   TYR B  88 
 PHE   0.010   0.001   PHE A 101 
 TRP   0.005   0.001   TRP K 536 
 HIS   0.004   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (13258)
  covalent geometry    : angle       0.58755 (19135)
  hydrogen bonds       : bond        0.05463 (  744)
  hydrogen bonds       : angle       2.91222 ( 1854)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A  111 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8292 (mp)
REVERT: B   91 LYS cc_start: 0.8277 (ttpt) cc_final: 0.7824 (tmtt)
REVERT: C   65 GLU cc_start: 0.8622 (tt0) cc_final: 0.8303 (tt0)
REVERT: D   99 ARG cc_start: 0.8750 (mtm-85) cc_final: 0.8352 (mtm-85)
REVERT: E   48 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8803 (mm)
REVERT: E   49 ARG cc_start: 0.8235 (mtm110) cc_final: 0.8010 (ttp-110)
REVERT: E   89 MET cc_start: 0.7876 (mmm) cc_final: 0.7380 (mmt)
REVERT: E  108 ASP cc_start: 0.8122 (m-30) cc_final: 0.7901 (m-30)
REVERT: H   34 LYS cc_start: 0.7594 (tptt) cc_final: 0.6499 (mttt)
  outliers start: 15
  outliers final: 11
  residues processed: 101
  average time/residue: 0.1716
  time to fit residues: 22.6864
Evaluate side-chains
  93 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain K residue  534 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 87 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   chunk 84 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 77 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 48 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
F  25 ASN
H  49 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.174661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.138486 restraints weight = 15024.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 0.88
r_work: 0.3109 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.3348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13258  Z= 0.179
  Angle     :  0.579   6.536  19135  Z= 0.348
  Chirality :  0.037   0.171   2165
  Planarity :  0.004   0.052   1429
  Dihedral  : 31.372 124.824   4056
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 15.28 %
    Favored  : 81.80 %
  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 are not related in a simple way.
  whole:  2.38 (0.29), residues: 804
  helix:  2.70 (0.22), residues: 520
  sheet:  None (None), residues: 0
  loop : -0.62 (0.34), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 524 
 TYR   0.019   0.001   TYR B  88 
 PHE   0.010   0.001   PHE A 101 
 TRP   0.004   0.001   TRP K 536 
 HIS   0.003   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 (13258)
  covalent geometry    : angle       0.57863 (19135)
  hydrogen bonds       : bond        0.05403 (  744)
  hydrogen bonds       : angle       2.88150 ( 1854)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A  111 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8327 (mp)
REVERT: B   91 LYS cc_start: 0.8369 (ttpt) cc_final: 0.7884 (tmtt)
REVERT: C   65 GLU cc_start: 0.8640 (tt0) cc_final: 0.8326 (tt0)
REVERT: D   99 ARG cc_start: 0.8732 (mtm-85) cc_final: 0.8377 (mtm-85)
REVERT: E   48 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8778 (mm)
REVERT: E   89 MET cc_start: 0.7901 (mmm) cc_final: 0.7415 (mmt)
REVERT: E  108 ASP cc_start: 0.8111 (m-30) cc_final: 0.7795 (m-30)
REVERT: E  133 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7246 (ptt180)
REVERT: H   34 LYS cc_start: 0.7565 (tptt) cc_final: 0.6438 (mtpt)
REVERT: K  521 ILE cc_start: 0.3599 (OUTLIER) cc_final: 0.3215 (mm)
  outliers start: 20
  outliers final: 14
  residues processed: 99
  average time/residue: 0.1834
  time to fit residues: 23.5195
Evaluate side-chains
  100 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain E residue  133 ARG
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain G residue   62 GLU
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain K residue  521 ILE
Chi-restraints excluded: chain K residue  534 SER
Chi-restraints excluded: chain L residue  533 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 17 optimal weight:    8.9990
   chunk 6 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 93 optimal weight:   10.0000
   chunk 37 optimal weight:   10.0000
   chunk 102 optimal weight:    9.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
C  25 GLN
D  47 GLN
D  49 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.178003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.141672 restraints weight = 15210.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 0.90
r_work: 0.3158 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.3470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13258  Z= 0.152
  Angle     :  0.543   6.538  19135  Z= 0.330
  Chirality :  0.036   0.170   2165
  Planarity :  0.004   0.050   1429
  Dihedral  : 31.147 126.951   4056
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.03 %
    Favored  : 80.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.63 (0.29), residues: 804
  helix:  2.89 (0.22), residues: 521
  sheet:  None (None), residues: 0
  loop : -0.52 (0.34), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  80 
 TYR   0.013   0.001   TYR B  88 
 PHE   0.007   0.001   PHE A 101 
 TRP   0.004   0.001   TRP K 536 
 HIS   0.003   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (13258)
  covalent geometry    : angle       0.54316 (19135)
  hydrogen bonds       : bond        0.04584 (  744)
  hydrogen bonds       : angle       2.73315 ( 1854)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A  111 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8254 (mp)
REVERT: B   91 LYS cc_start: 0.8285 (ttpt) cc_final: 0.7839 (tmtt)
REVERT: C   65 GLU cc_start: 0.8570 (tt0) cc_final: 0.8271 (tt0)
REVERT: D   99 ARG cc_start: 0.8688 (mtm-85) cc_final: 0.8445 (mtm-85)
REVERT: E   48 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8763 (mm)
REVERT: E   89 MET cc_start: 0.7893 (mmm) cc_final: 0.7367 (mmt)
REVERT: E  108 ASP cc_start: 0.8027 (m-30) cc_final: 0.7734 (m-30)
REVERT: E  133 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7153 (ptt180)
REVERT: H   34 LYS cc_start: 0.7576 (tptt) cc_final: 0.6502 (mtpt)
REVERT: K  521 ILE cc_start: 0.3936 (OUTLIER) cc_final: 0.3508 (mm)
  outliers start: 17
  outliers final: 10
  residues processed: 94
  average time/residue: 0.1867
  time to fit residues: 22.6061
Evaluate side-chains
  92 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain E residue  133 ARG
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain G residue   62 GLU
Chi-restraints excluded: chain K residue  521 ILE
Chi-restraints excluded: chain K residue  534 SER
Chi-restraints excluded: chain L residue  533 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    3.9990
   chunk 37 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 97 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   overall best weight:    3.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.171676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.135277 restraints weight = 15008.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 0.97
r_work: 0.3057 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.3870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  13258  Z= 0.225
  Angle     :  0.625   6.541  19135  Z= 0.372
  Chirality :  0.040   0.176   2165
  Planarity :  0.005   0.063   1429
  Dihedral  : 31.440 124.212   4056
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 17.18 %
    Favored  : 79.62 %
  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 are not related in a simple way.
  whole:  2.20 (0.29), residues: 804
  helix:  2.55 (0.22), residues: 521
  sheet: -2.40 (1.26), residues: 20
  loop : -0.51 (0.36), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  80 
 TYR   0.014   0.002   TYR B  88 
 PHE   0.011   0.002   PHE A 101 
 TRP   0.003   0.001   TRP A  86 
 HIS   0.004   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 (13258)
  covalent geometry    : angle       0.62539 (19135)
  hydrogen bonds       : bond        0.06349 (  744)
  hydrogen bonds       : angle       2.96648 ( 1854)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A  111 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8417 (mp)
REVERT: B   91 LYS cc_start: 0.8366 (ttpt) cc_final: 0.7923 (ttpp)
REVERT: C   65 GLU cc_start: 0.8601 (tt0) cc_final: 0.8261 (tt0)
REVERT: C   73 ASP cc_start: 0.7652 (t70) cc_final: 0.7304 (t0)
REVERT: D   99 ARG cc_start: 0.8645 (mtm-85) cc_final: 0.8381 (mtm-85)
REVERT: E   48 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8803 (mm)
REVERT: E   53 ARG cc_start: 0.8286 (ttp80) cc_final: 0.8042 (ttp-110)
REVERT: E   89 MET cc_start: 0.8034 (mmm) cc_final: 0.7485 (mmt)
REVERT: E  108 ASP cc_start: 0.8183 (m-30) cc_final: 0.7886 (m-30)
REVERT: E  133 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7369 (ptt180)
REVERT: H   34 LYS cc_start: 0.7499 (tptt) cc_final: 0.6405 (mtpt)
REVERT: K  521 ILE cc_start: 0.4073 (OUTLIER) cc_final: 0.3609 (mm)
REVERT: L  549 VAL cc_start: 0.6953 (p) cc_final: 0.6682 (t)
  outliers start: 22
  outliers final: 13
  residues processed: 99
  average time/residue: 0.2000
  time to fit residues: 25.1179
Evaluate side-chains
  94 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain E residue   83 ASP
Chi-restraints excluded: chain E residue  133 ARG
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain K residue  521 ILE
Chi-restraints excluded: chain K residue  534 SER
Chi-restraints excluded: chain L residue  533 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 81 optimal weight:    9.9990
   chunk 105 optimal weight:    9.9990
   chunk 33 optimal weight:    2.9990
   chunk 19 optimal weight:    0.4980
   chunk 46 optimal weight:    0.4980
   chunk 91 optimal weight:   10.0000
   chunk 79 optimal weight:   10.0000
   chunk 24 optimal weight:    0.0030
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.9792

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.177918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.141335 restraints weight = 15064.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 0.91
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.3906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  13258  Z= 0.151
  Angle     :  0.543   6.684  19135  Z= 0.329
  Chirality :  0.035   0.173   2165
  Planarity :  0.004   0.049   1429
  Dihedral  : 31.057 127.461   4056
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 17.32 %
    Favored  : 80.06 %
  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 are not related in a simple way.
  whole:  2.59 (0.30), residues: 804
  helix:  2.88 (0.22), residues: 522
  sheet: -2.25 (1.32), residues: 20
  loop : -0.42 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  86 
 TYR   0.011   0.001   TYR B  88 
 PHE   0.008   0.001   PHE A 101 
 TRP   0.004   0.001   TRP L 536 
 HIS   0.002   0.001   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (13258)
  covalent geometry    : angle       0.54261 (19135)
  hydrogen bonds       : bond        0.04509 (  744)
  hydrogen bonds       : angle       2.73062 ( 1854)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A  111 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8254 (mp)
REVERT: B   91 LYS cc_start: 0.8057 (ttpt) cc_final: 0.7642 (tmtt)
REVERT: C   65 GLU cc_start: 0.7694 (tt0) cc_final: 0.7412 (tt0)
REVERT: E   89 MET cc_start: 0.7040 (mmm) cc_final: 0.6475 (mmt)
REVERT: E  108 ASP cc_start: 0.7631 (m-30) cc_final: 0.7319 (m-30)
REVERT: E  133 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.6936 (ptt180)
REVERT: H   34 LYS cc_start: 0.7454 (tptt) cc_final: 0.6692 (mtpt)
REVERT: L  549 VAL cc_start: 0.7088 (p) cc_final: 0.6861 (t)
  outliers start: 18
  outliers final: 11
  residues processed: 94
  average time/residue: 0.1796
  time to fit residues: 21.8146
Evaluate side-chains
  93 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   83 ASP
Chi-restraints excluded: chain E residue  133 ARG
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain K residue  534 SER
Chi-restraints excluded: chain L residue  533 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 51 optimal weight:    0.1980
   chunk 16 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   overall best weight:    1.4186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.176455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.139133 restraints weight = 14943.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 0.89
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.4012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13258  Z= 0.161
  Angle     :  0.554   7.913  19135  Z= 0.332
  Chirality :  0.036   0.222   2165
  Planarity :  0.004   0.049   1429
  Dihedral  : 31.088 127.727   4056
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 17.47 %
    Favored  : 80.35 %
  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 are not related in a simple way.
  whole:  2.59 (0.30), residues: 804
  helix:  2.85 (0.22), residues: 522
  sheet: -2.25 (1.30), residues: 20
  loop : -0.37 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  35 
 TYR   0.009   0.001   TYR B  51 
 PHE   0.009   0.001   PHE A 101 
 TRP   0.003   0.001   TRP K 536 
 HIS   0.002   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (13258)
  covalent geometry    : angle       0.55386 (19135)
  hydrogen bonds       : bond        0.04869 (  744)
  hydrogen bonds       : angle       2.79535 ( 1854)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A  111 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8346 (mp)
REVERT: B   91 LYS cc_start: 0.8042 (ttpt) cc_final: 0.7619 (tmtt)
REVERT: C   65 GLU cc_start: 0.7747 (tt0) cc_final: 0.7466 (tt0)
REVERT: D  119 THR cc_start: 0.8697 (m) cc_final: 0.8369 (p)
REVERT: E   45 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8324 (m)
REVERT: E   89 MET cc_start: 0.7088 (mmm) cc_final: 0.6482 (mmt)
REVERT: E  108 ASP cc_start: 0.7644 (m-30) cc_final: 0.7330 (m-30)
REVERT: E  133 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.6928 (ptt180)
REVERT: H   34 LYS cc_start: 0.7498 (tptt) cc_final: 0.6705 (mtpt)
REVERT: L  549 VAL cc_start: 0.7059 (p) cc_final: 0.6770 (t)
  outliers start: 15
  outliers final: 11
  residues processed: 88
  average time/residue: 0.1902
  time to fit residues: 21.5758
Evaluate side-chains
  89 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   83 ASP
Chi-restraints excluded: chain E residue  133 ARG
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain G residue   62 GLU
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain K residue  534 SER
Chi-restraints excluded: chain L residue  533 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0670
   chunk 44 optimal weight:    2.9990
   chunk 78 optimal weight:   10.0000
   chunk 14 optimal weight:    0.8980
   chunk 57 optimal weight:    7.9990
   chunk 25 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 49 optimal weight:    6.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.7118

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.178130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.140848 restraints weight = 15045.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 0.83
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.4036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  13258  Z= 0.147
  Angle     :  0.540   7.930  19135  Z= 0.326
  Chirality :  0.036   0.166   2165
  Planarity :  0.004   0.049   1429
  Dihedral  : 31.027 129.353   4056
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 17.61 %
    Favored  : 80.35 %
  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 are not related in a simple way.
  whole:  2.68 (0.30), residues: 804
  helix:  2.93 (0.22), residues: 523
  sheet: -2.25 (1.27), residues: 20
  loop : -0.35 (0.36), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 117 
 TYR   0.011   0.001   TYR B  88 
 PHE   0.007   0.001   PHE F  61 
 TRP   0.003   0.001   TRP K 536 
 HIS   0.002   0.000   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (13258)
  covalent geometry    : angle       0.53966 (19135)
  hydrogen bonds       : bond        0.04507 (  744)
  hydrogen bonds       : angle       2.76373 ( 1854)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A  111 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8279 (mp)
REVERT: B   91 LYS cc_start: 0.8048 (ttpt) cc_final: 0.7627 (tmtt)
REVERT: C   65 GLU cc_start: 0.7724 (tt0) cc_final: 0.7435 (tt0)
REVERT: D  119 THR cc_start: 0.8672 (m) cc_final: 0.8380 (p)
REVERT: E   89 MET cc_start: 0.7050 (mmm) cc_final: 0.6450 (mmt)
REVERT: E  108 ASP cc_start: 0.7624 (m-30) cc_final: 0.7318 (m-30)
REVERT: E  133 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.6913 (ptt180)
REVERT: H   34 LYS cc_start: 0.7488 (tptt) cc_final: 0.6698 (mtpt)
  outliers start: 14
  outliers final: 11
  residues processed: 87
  average time/residue: 0.1723
  time to fit residues: 19.3470
Evaluate side-chains
  89 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain E residue   62 ILE
Chi-restraints excluded: chain E residue   83 ASP
Chi-restraints excluded: chain E residue  133 ARG
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain G residue   62 GLU
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain L residue  533 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 92 optimal weight:   10.0000
   chunk 32 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 82 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 11 optimal weight:    0.2980
   chunk 27 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   chunk 97 optimal weight:   10.0000
   overall best weight:    2.2386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.173967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.136323 restraints weight = 14989.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 0.90
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.4222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  13258  Z= 0.188
  Angle     :  0.594   7.402  19135  Z= 0.353
  Chirality :  0.038   0.181   2165
  Planarity :  0.004   0.058   1429
  Dihedral  : 31.242 127.193   4056
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 17.76 %
    Favored  : 80.64 %
  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 are not related in a simple way.
  whole:  2.46 (0.30), residues: 804
  helix:  2.76 (0.22), residues: 521
  sheet: -2.26 (1.28), residues: 20
  loop : -0.40 (0.36), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  40 
 TYR   0.010   0.001   TYR B  51 
 PHE   0.010   0.001   PHE A 101 
 TRP   0.003   0.001   TRP E  86 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 (13258)
  covalent geometry    : angle       0.59391 (19135)
  hydrogen bonds       : bond        0.05687 (  744)
  hydrogen bonds       : angle       2.89753 ( 1854)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A  111 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8412 (mp)
REVERT: B   91 LYS cc_start: 0.8151 (ttpt) cc_final: 0.7686 (tmtt)
REVERT: C   65 GLU cc_start: 0.7752 (tt0) cc_final: 0.7418 (tt0)
REVERT: E   89 MET cc_start: 0.7065 (mmm) cc_final: 0.6476 (mmt)
REVERT: E  133 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7075 (ptt180)
REVERT: H   34 LYS cc_start: 0.7506 (tptt) cc_final: 0.6685 (mtpt)
  outliers start: 11
  outliers final: 9
  residues processed: 84
  average time/residue: 0.1890
  time to fit residues: 20.3055
Evaluate side-chains
  83 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain E residue   83 ASP
Chi-restraints excluded: chain E residue  133 ARG
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain L residue  533 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 1 optimal weight:    0.0980
   chunk 77 optimal weight:    5.9990
   chunk 95 optimal weight:   10.0000
   chunk 89 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 99 optimal weight:   10.0000
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 102 optimal weight:    9.9990
   chunk 11 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.177352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.140392 restraints weight = 14957.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 0.89
r_work: 0.3150 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.4250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13258  Z= 0.153
  Angle     :  0.550   7.131  19135  Z= 0.331
  Chirality :  0.036   0.172   2165
  Planarity :  0.004   0.047   1429
  Dihedral  : 31.055 129.060   4056
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 18.05 %
    Favored  : 80.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.61 (0.30), residues: 804
  helix:  2.89 (0.22), residues: 520
  sheet: -1.98 (1.28), residues: 20
  loop : -0.41 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 117 
 TYR   0.008   0.001   TYR D  42 
 PHE   0.007   0.001   PHE F  61 
 TRP   0.004   0.001   TRP L 536 
 HIS   0.003   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (13258)
  covalent geometry    : angle       0.55011 (19135)
  hydrogen bonds       : bond        0.04705 (  744)
  hydrogen bonds       : angle       2.78568 ( 1854)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2126.90 seconds
wall clock time: 37 minutes 11.26 seconds (2231.26 seconds total)