Starting phenix.real_space_refine
on Fri Aug 22 15:06:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jc0_36149/08_2025/8jc0_36149.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jc0_36149/08_2025/8jc0_36149.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jc0_36149/08_2025/8jc0_36149.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jc0_36149/08_2025/8jc0_36149.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jc0_36149/08_2025/8jc0_36149.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jc0_36149/08_2025/8jc0_36149.cif"
  }
  resolution = 3.4
  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=   0.073
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    3048      2.51       5
     N     741      2.21       5
     O     865      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s

  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: 4691
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "a"
      Number of atoms: 251
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 251
          Classifications: {'peptide': 31}
          Link IDs: {'PTRANS': 1, 'TRANS': 29}
    Chain: "b"
      Number of atoms: 226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 226
          Classifications: {'peptide': 28}
          Link IDs: {'PTRANS': 1, 'TRANS': 26}
    Chain: "d"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 817
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 3, 'TRANS': 101}
    Chain: "e"
      Number of atoms: 959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 959
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 5, 'TRANS': 115}
    Chain: "f"
      Number of atoms: 933
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 933
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 5, 'TRANS': 112}
          Chain breaks: 1
    Chain: "g"
      Number of atoms: 907
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 907
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 2, 'TRANS': 112}
    Chain: "m"
      Number of atoms: 268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 268
          Classifications: {'peptide': 34}
          Link IDs: {'TRANS': 33}
    Chain: "n"
      Number of atoms: 302
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 302
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "m"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.25, per 1000 atoms: 0.27
  Number of scatterers: 4691
  At special positions: 0
  Unit cell: (69.568, 91.308, 105.439, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O     865      8.00
     N     741      7.00
     C    3048      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS a  32 " - pdb=" SG  CYS b  32 " distance=2.04
    Simple disulfide: pdb=" SG  CYS d  37 " - pdb=" SG  CYS d  73 " distance=2.03
    Simple disulfide: pdb=" SG  CYS d  93 " - pdb=" SG  CYS d  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS e  49 " - pdb=" SG  CYS e  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS e 119 " - pdb=" SG  CYS e 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS f  49 " - pdb=" SG  CYS f  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS f 119 " - pdb=" SG  CYS f 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS g  46 " - pdb=" SG  CYS g  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS g 104 " - pdb=" SG  CYS g 107 " distance=2.03

  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: 0.41
  Conformation dependent library (CDL) restraints added in 186.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1098

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 10 sheets defined
      39.7% alpha, 16.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'a' and resid 31 through 56
      removed outlier: 3.949A  pdb=" N   LEU a  35 " --> pdb=" O   LEU a  31 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 28 through 52
      removed outlier: 4.047A  pdb=" N   CYS b  32 " --> pdb=" O   ASP b  28 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   TYR b  33 " --> pdb=" O   PRO b  29 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU b  34 " --> pdb=" O   LYS b  30 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   GLY b  37 " --> pdb=" O   TYR b  33 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 100 through 126
      removed outlier: 4.464A  pdb=" N   THR d 110 " --> pdb=" O   GLY d 106 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ILE d 113 " --> pdb=" O   VAL d 109 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLY d 121 " --> pdb=" O   LEU d 117 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   VAL d 122 " --> pdb=" O   LEU d 118 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   PHE d 123 " --> pdb=" O   ALA d 119 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 104 through 108
      removed outlier: 4.083A  pdb=" N   ALA e 108 " --> pdb=" O   PRO e 105 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 127 through 151
      removed outlier: 4.199A  pdb=" N   ILE e 133 " --> pdb=" O   SER e 129 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   TYR e 150 " --> pdb=" O   LEU e 146 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 104 through 108
    Processing helix  chain 'f' and resid 132 through 154
      removed outlier: 3.951A  pdb=" N   LEU f 147 " --> pdb=" O   GLY f 143 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ASN f 154 " --> pdb=" O   TYR f 150 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 78 through 80
      No H-bonds generated for 'chain 'g' and resid 78 through 80'
    Processing helix  chain 'g' and resid 113 through 140
      removed outlier: 3.799A  pdb=" N   VAL g 124 " --> pdb=" O   PHE g 120 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   SER g 125 " --> pdb=" O   ALA g 121 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   ILE g 126 " --> pdb=" O   GLU g 122 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   PHE g 135 " --> pdb=" O   VAL g 131 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 258 through 289
      removed outlier: 3.892A  pdb=" N   ALA m 278 " --> pdb=" O   ALA m 274 " (cutoff:3.500A)
    Processing helix  chain 'n' and resid 253 through 269
      removed outlier: 3.762A  pdb=" N   LEU n 257 " --> pdb=" O   LEU n 253 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   THR n 260 " --> pdb=" O   GLN n 256 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   TYR n 264 " --> pdb=" O   THR n 260 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   MET n 265 " --> pdb=" O   SER n 261 " (cutoff:3.500A)
    Processing helix  chain 'n' and resid 269 through 286
      removed outlier: 3.685A  pdb=" N   SER n 273 " --> pdb=" O   LEU n 269 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL n 274 " --> pdb=" O   LEU n 270 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   VAL n 275 " --> pdb=" O   LEU n 271 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ARG n 286 " --> pdb=" O   CYS n 282 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'd' and resid 32 through 36
      removed outlier: 6.449A  pdb=" N   VAL d  33 " --> pdb=" O   LEU d  60 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'd' and resid 42 through 46
      removed outlier: 5.218A  pdb=" N   TRP d  43 " --> pdb=" O   ARG d  72 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   ARG d  72 " --> pdb=" O   TRP d  43 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   VAL d  86 " --> pdb=" O   TYR d  71 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'e' and resid 38 through 41
      removed outlier: 3.501A  pdb=" N   GLY e  76 " --> pdb=" O   SER e  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'e' and resid 57 through 59
      removed outlier: 3.676A  pdb=" N   TYR e  99 " --> pdb=" O   LEU e  58 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'f' and resid 37 through 41
      removed outlier: 3.712A  pdb=" N   GLY f  76 " --> pdb=" O   SER f  83 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'f' and resid 65 through 66
      removed outlier: 3.707A  pdb=" N   TRP f  59 " --> pdb=" O   ILE f  66 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   TYR f  99 " --> pdb=" O   LEU f  58 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLN f  60 " --> pdb=" O   VAL f  97 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL f  97 " --> pdb=" O   GLN f  60 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'f' and resid 111 through 114
      removed outlier: 6.473A  pdb=" N   TYR f 111 " --> pdb=" O   GLN g  98 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   TYR g 100 " --> pdb=" O   TYR f 111 " (cutoff:3.500A)
      removed outlier: 5.722A  pdb=" N   TYR f 113 " --> pdb=" O   TYR g 100 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   TYR g  85 " --> pdb=" O   LEU g  97 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   GLN g  86 " --> pdb=" O   PHE g  56 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'f' and resid 122 through 123
      removed outlier: 3.577A  pdb=" N   MET f 123 " --> pdb=" O   ILE g 108 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'g' and resid 31 through 34
      removed outlier: 3.722A  pdb=" N   LEU g  43 " --> pdb=" O   TYR g  34 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   VAL g  42 " --> pdb=" O   LEU g  74 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU g  74 " --> pdb=" O   VAL g  42 " (cutoff:3.500A)

    212 hydrogen bonds defined for protein.
    597 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.53

  Time building geometry restraints manager: 0.55 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1449
        1.34 -     1.47: 1131
        1.47 -     1.59: 2148
        1.59 -     1.71: 2
        1.71 -     1.83: 51
  Bond restraints: 4781
  Sorted by residual:
  bond pdb=" CB  PRO f  50 "
       pdb=" CG  PRO f  50 "
    ideal  model  delta    sigma   weight residual
    1.492  1.607 -0.115 5.00e-02 4.00e+02 5.27e+00
  bond pdb=" CB  PRO f  35 "
       pdb=" CG  PRO f  35 "
    ideal  model  delta    sigma   weight residual
    1.492  1.602 -0.110 5.00e-02 4.00e+02 4.85e+00
  bond pdb=" CA  ASP f  80 "
       pdb=" CB  ASP f  80 "
    ideal  model  delta    sigma   weight residual
    1.533  1.560 -0.026 2.15e-02 2.16e+03 1.49e+00
  bond pdb=" N   VAL d  33 "
       pdb=" CA  VAL d  33 "
    ideal  model  delta    sigma   weight residual
    1.459  1.473 -0.014 1.24e-02 6.50e+03 1.35e+00
  bond pdb=" CA  ASP d  66 "
       pdb=" CB  ASP d  66 "
    ideal  model  delta    sigma   weight residual
    1.522  1.530 -0.008 7.00e-03 2.04e+04 1.31e+00
  ... (remaining 4776 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.54: 6425
        2.54 -     5.08: 43
        5.08 -     7.61: 9
        7.61 -    10.15: 1
       10.15 -    12.69: 2
  Bond angle restraints: 6480
  Sorted by residual:
  angle pdb=" CA  PRO f  50 "
        pdb=" N   PRO f  50 "
        pdb=" CD  PRO f  50 "
      ideal   model   delta    sigma   weight residual
     112.00  106.32    5.68 1.40e+00 5.10e-01 1.65e+01
  angle pdb=" CA  PRO f  35 "
        pdb=" N   PRO f  35 "
        pdb=" CD  PRO f  35 "
      ideal   model   delta    sigma   weight residual
     112.00  106.90    5.10 1.40e+00 5.10e-01 1.33e+01
  angle pdb=" CA  LEU d  29 "
        pdb=" CB  LEU d  29 "
        pdb=" CG  LEU d  29 "
      ideal   model   delta    sigma   weight residual
     116.30  128.99  -12.69 3.50e+00 8.16e-02 1.31e+01
  angle pdb=" CB  MET f 128 "
        pdb=" CG  MET f 128 "
        pdb=" SD  MET f 128 "
      ideal   model   delta    sigma   weight residual
     112.70  123.48  -10.78 3.00e+00 1.11e-01 1.29e+01
  angle pdb=" CA  MET f 128 "
        pdb=" CB  MET f 128 "
        pdb=" CG  MET f 128 "
      ideal   model   delta    sigma   weight residual
     114.10  120.63   -6.53 2.00e+00 2.50e-01 1.07e+01
  ... (remaining 6475 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 2531
       17.94 -    35.89: 300
       35.89 -    53.83: 65
       53.83 -    71.77: 11
       71.77 -    89.71: 7
  Dihedral angle restraints: 2914
    sinusoidal: 1201
      harmonic: 1713
  Sorted by residual:
  dihedral pdb=" CB  CYS d  37 "
           pdb=" SG  CYS d  37 "
           pdb=" SG  CYS d  73 "
           pdb=" CB  CYS d  73 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -165.61   79.61     1      1.00e+01 1.00e-02 7.87e+01
  dihedral pdb=" CB  CYS e 119 "
           pdb=" SG  CYS e 119 "
           pdb=" SG  CYS e 122 "
           pdb=" CB  CYS e 122 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  157.36  -64.36     1      1.00e+01 1.00e-02 5.45e+01
  dihedral pdb=" CB  CYS g 104 "
           pdb=" SG  CYS g 104 "
           pdb=" SG  CYS g 107 "
           pdb=" CB  CYS g 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -142.71   56.71     1      1.00e+01 1.00e-02 4.33e+01
  ... (remaining 2911 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 471
       0.030 -    0.059: 200
       0.059 -    0.089: 58
       0.089 -    0.119: 26
       0.119 -    0.148: 6
  Chirality restraints: 761
  Sorted by residual:
  chirality pdb=" CA  ASP f  80 "
            pdb=" N   ASP f  80 "
            pdb=" C   ASP f  80 "
            pdb=" CB  ASP f  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.51e-01
  chirality pdb=" CA  ASN f 121 "
            pdb=" N   ASN f 121 "
            pdb=" C   ASN f 121 "
            pdb=" CB  ASN f 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.85e-01
  chirality pdb=" CA  ILE d  70 "
            pdb=" N   ILE d  70 "
            pdb=" C   ILE d  70 "
            pdb=" CB  ILE d  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.77e-01
  ... (remaining 758 not shown)

  Planarity restraints: 793
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS f  49 "   -0.037 5.00e-02 4.00e+02   5.35e-02 4.59e+00
        pdb=" N   PRO f  50 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO f  50 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO f  50 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR f  34 "    0.029 5.00e-02 4.00e+02   4.21e-02 2.84e+00
        pdb=" N   PRO f  35 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO f  35 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO f  35 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP d 100 "    0.026 5.00e-02 4.00e+02   4.05e-02 2.62e+00
        pdb=" N   PRO d 101 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO d 101 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO d 101 "    0.022 5.00e-02 4.00e+02
  ... (remaining 790 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 773
        2.77 -     3.30: 4375
        3.30 -     3.83: 7211
        3.83 -     4.37: 7945
        4.37 -     4.90: 14200
  Nonbonded interactions: 34504
  Sorted by model distance:
  nonbonded pdb=" O   CYS d  93 "
            pdb=" NH1 ARG e 117 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" OH  TYR a  42 "
            pdb=" OG1 THR b  47 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OD2 ASP b  36 "
            pdb=" OH  TYR n 266 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   ARG g  82 "
            pdb=" OH  TYR g  85 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" O   ALA f 108 "
            pdb=" NZ  LYS g  95 "
     model   vdw
     2.312 3.120
  ... (remaining 34499 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 27 through 54)
  selection = chain 'b'
}
ncs_group {
  reference = (chain 'e' and (resid 33 through 69 or resid 74 through 153))
  selection = (chain 'f' and resid 33 through 153)
}

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:             0.490
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.820
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5221
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      :  0.003   0.115   4790  Z= 0.143
  Angle     :  0.655  12.690   6498  Z= 0.369
  Chirality :  0.039   0.148    761
  Planarity :  0.004   0.054    793
  Dihedral  : 15.868  89.715   1789
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 21.80 %
    Favored  : 78.20 %
  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: -1.74 (0.35), residues: 571
  helix:  0.88 (0.37), residues: 213
  sheet: -2.09 (0.47), residues: 117
  loop : -2.57 (0.35), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG d  63 
 TYR   0.009   0.001   TYR d  71 
 PHE   0.006   0.001   PHE m 281 
 TRP   0.023   0.001   TRP d  43 
 HIS   0.004   0.001   HIS f  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 4781)
  covalent geometry    : angle       0.65216 ( 6480)
  SS BOND              : bond        0.00223 (    9)
  SS BOND              : angle       1.25126 (   18)
  hydrogen bonds       : bond        0.20981 (  212)
  hydrogen bonds       : angle       6.78326 (  597)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0673
  time to fit residues: 5.1352
Evaluate side-chains
  59 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0970
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
e  51 GLN
e  81 HIS
f  61 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.229665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.186498 restraints weight = 4512.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.4117 rms_B_bonded: 2.04
r_work: 0.3957 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3797 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.0836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   4790  Z= 0.124
  Angle     :  0.566   9.868   6498  Z= 0.292
  Chirality :  0.040   0.149    761
  Planarity :  0.003   0.032    793
  Dihedral  :  4.472  31.987    699
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 18.74 %
    Favored  : 79.16 %
  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: -1.42 (0.35), residues: 571
  helix:  1.40 (0.37), residues: 215
  sheet: -2.14 (0.48), residues: 107
  loop : -2.57 (0.34), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG d  68 
 TYR   0.012   0.001   TYR n 263 
 PHE   0.006   0.001   PHE f 110 
 TRP   0.013   0.001   TRP d  43 
 HIS   0.004   0.001   HIS f  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 4781)
  covalent geometry    : angle       0.56437 ( 6480)
  SS BOND              : bond        0.00257 (    9)
  SS BOND              : angle       1.04432 (   18)
  hydrogen bonds       : bond        0.04619 (  212)
  hydrogen bonds       : angle       4.48278 (  597)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.170 
Fit side-chains
REVERT: a   30 LYS cc_start: 0.7335 (ptpt) cc_final: 0.6192 (tptp)
REVERT: g   71 LYS cc_start: 0.7577 (mttt) cc_final: 0.7228 (mttt)
  outliers start: 11
  outliers final: 6
  residues processed: 64
  average time/residue: 0.0732
  time to fit residues: 6.1321
Evaluate side-chains
  59 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   27 LEU
Chi-restraints excluded: chain d residue   71 TYR
Chi-restraints excluded: chain e residue  118 VAL
Chi-restraints excluded: chain e residue  119 CYS
Chi-restraints excluded: chain f residue   39 SER
Chi-restraints excluded: chain n residue  257 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 21 optimal weight:    0.4980
   chunk 33 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
e  81 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.224551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.177566 restraints weight = 4493.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.4009 rms_B_bonded: 2.37
r_work: 0.3884 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3710 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7173
moved from start:          0.1349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4790  Z= 0.148
  Angle     :  0.597   8.209   6498  Z= 0.299
  Chirality :  0.041   0.147    761
  Planarity :  0.003   0.029    793
  Dihedral  :  4.902  43.961    699
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 17.97 %
    Favored  : 78.59 %
  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: -1.42 (0.35), residues: 571
  helix:  1.38 (0.36), residues: 216
  sheet: -2.15 (0.46), residues: 120
  loop : -2.54 (0.36), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG e 117 
 TYR   0.015   0.001   TYR n 263 
 PHE   0.009   0.001   PHE f 110 
 TRP   0.014   0.001   TRP d  43 
 HIS   0.003   0.001   HIS f  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 4781)
  covalent geometry    : angle       0.59492 ( 6480)
  SS BOND              : bond        0.00240 (    9)
  SS BOND              : angle       1.08258 (   18)
  hydrogen bonds       : bond        0.04099 (  212)
  hydrogen bonds       : angle       4.09295 (  597)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 55
  time to evaluate  : 0.178 
Fit side-chains
REVERT: a   30 LYS cc_start: 0.7045 (ptpt) cc_final: 0.5886 (tptp)
REVERT: a   45 ILE cc_start: 0.8369 (mt) cc_final: 0.8126 (mp)
REVERT: e  123 MET cc_start: 0.7258 (ptp) cc_final: 0.6820 (ptm)
REVERT: f   90 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.7009 (mm)
REVERT: f  128 MET cc_start: 0.5502 (tpp) cc_final: 0.5135 (tpp)
REVERT: g   71 LYS cc_start: 0.7532 (mttt) cc_final: 0.7133 (mttt)
  outliers start: 18
  outliers final: 11
  residues processed: 68
  average time/residue: 0.0654
  time to fit residues: 5.9082
Evaluate side-chains
  66 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   27 LEU
Chi-restraints excluded: chain a residue   32 CYS
Chi-restraints excluded: chain b residue   40 PHE
Chi-restraints excluded: chain b residue   46 LEU
Chi-restraints excluded: chain d residue   37 CYS
Chi-restraints excluded: chain d residue   68 ARG
Chi-restraints excluded: chain e residue   98 CYS
Chi-restraints excluded: chain e residue  118 VAL
Chi-restraints excluded: chain e residue  119 CYS
Chi-restraints excluded: chain f residue   39 SER
Chi-restraints excluded: chain f residue   90 LEU
Chi-restraints excluded: chain n residue  257 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   chunk 43 optimal weight:    0.2980
   chunk 30 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0060
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.2602

-------------------------------------------------------------------------------
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 = 0.4427 r_free = 0.4427 target = 0.220453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.173633 restraints weight = 4538.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3964 rms_B_bonded: 2.34
r_work: 0.3838 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3661 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start:          0.1694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4790  Z= 0.166
  Angle     :  0.594   6.386   6498  Z= 0.301
  Chirality :  0.042   0.154    761
  Planarity :  0.003   0.028    793
  Dihedral  :  5.198  51.411    699
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 18.74 %
    Favored  : 77.44 %
  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: -1.49 (0.36), residues: 571
  helix:  1.25 (0.36), residues: 215
  sheet: -2.04 (0.47), residues: 117
  loop : -2.57 (0.37), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG g  82 
 TYR   0.018   0.001   TYR n 263 
 PHE   0.011   0.001   PHE f 110 
 TRP   0.016   0.001   TRP d  43 
 HIS   0.002   0.001   HIS f  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 4781)
  covalent geometry    : angle       0.59230 ( 6480)
  SS BOND              : bond        0.00239 (    9)
  SS BOND              : angle       1.08937 (   18)
  hydrogen bonds       : bond        0.04091 (  212)
  hydrogen bonds       : angle       4.03291 (  597)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 54
  time to evaluate  : 0.121 
Fit side-chains
REVERT: a   30 LYS cc_start: 0.6973 (ptpt) cc_final: 0.5881 (tptp)
REVERT: e  123 MET cc_start: 0.7325 (ptp) cc_final: 0.6867 (ptm)
REVERT: f   90 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7107 (mm)
REVERT: f  128 MET cc_start: 0.5941 (tpp) cc_final: 0.5171 (tpp)
REVERT: g   56 PHE cc_start: 0.7119 (m-10) cc_final: 0.6816 (m-10)
REVERT: g   71 LYS cc_start: 0.7634 (mttt) cc_final: 0.7265 (mttt)
REVERT: g   95 LYS cc_start: 0.8236 (tttt) cc_final: 0.8017 (tttt)
  outliers start: 20
  outliers final: 13
  residues processed: 69
  average time/residue: 0.0500
  time to fit residues: 4.7380
Evaluate side-chains
  68 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   27 LEU
Chi-restraints excluded: chain a residue   32 CYS
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain b residue   46 LEU
Chi-restraints excluded: chain d residue   37 CYS
Chi-restraints excluded: chain d residue   68 ARG
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue   98 CYS
Chi-restraints excluded: chain e residue  118 VAL
Chi-restraints excluded: chain e residue  119 CYS
Chi-restraints excluded: chain f residue   39 SER
Chi-restraints excluded: chain f residue   90 LEU
Chi-restraints excluded: chain g residue  105 GLN
Chi-restraints excluded: chain n residue  257 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 40 optimal weight:   10.0000
   chunk 53 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 19 optimal weight:    6.9990
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
e  81 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.223493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.178385 restraints weight = 4503.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.4020 rms_B_bonded: 2.12
r_work: 0.3859 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3691 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7213
moved from start:          0.1788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4790  Z= 0.129
  Angle     :  0.556   6.240   6498  Z= 0.282
  Chirality :  0.040   0.150    761
  Planarity :  0.003   0.026    793
  Dihedral  :  5.118  52.931    699
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 20.65 %
    Favored  : 75.72 %
  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: -1.26 (0.36), residues: 571
  helix:  1.43 (0.36), residues: 213
  sheet: -1.94 (0.48), residues: 115
  loop : -2.40 (0.37), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG e 117 
 TYR   0.014   0.001   TYR n 263 
 PHE   0.007   0.001   PHE m 288 
 TRP   0.013   0.001   TRP d  43 
 HIS   0.002   0.001   HIS f  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 4781)
  covalent geometry    : angle       0.55302 ( 6480)
  SS BOND              : bond        0.00235 (    9)
  SS BOND              : angle       1.19920 (   18)
  hydrogen bonds       : bond        0.03677 (  212)
  hydrogen bonds       : angle       3.87389 (  597)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 55
  time to evaluate  : 0.182 
Fit side-chains
REVERT: a   30 LYS cc_start: 0.7047 (ptpt) cc_final: 0.5953 (tptp)
REVERT: a   45 ILE cc_start: 0.8489 (mt) cc_final: 0.8272 (mp)
REVERT: e  123 MET cc_start: 0.7327 (ptp) cc_final: 0.6872 (ptm)
REVERT: f   90 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7089 (mm)
REVERT: f  128 MET cc_start: 0.6073 (tpp) cc_final: 0.5227 (tpp)
REVERT: g   71 LYS cc_start: 0.7621 (mttt) cc_final: 0.7248 (mttt)
REVERT: g   95 LYS cc_start: 0.8195 (mttt) cc_final: 0.7990 (tttt)
  outliers start: 19
  outliers final: 15
  residues processed: 68
  average time/residue: 0.0570
  time to fit residues: 5.0829
Evaluate side-chains
  70 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 54
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   27 LEU
Chi-restraints excluded: chain a residue   32 CYS
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain b residue   40 PHE
Chi-restraints excluded: chain b residue   46 LEU
Chi-restraints excluded: chain d residue   37 CYS
Chi-restraints excluded: chain d residue   68 ARG
Chi-restraints excluded: chain d residue   71 TYR
Chi-restraints excluded: chain d residue  109 VAL
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue   98 CYS
Chi-restraints excluded: chain e residue  118 VAL
Chi-restraints excluded: chain e residue  119 CYS
Chi-restraints excluded: chain f residue   39 SER
Chi-restraints excluded: chain f residue   90 LEU
Chi-restraints excluded: chain n residue  257 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 42 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 4 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
e  81 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.224990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.180171 restraints weight = 4584.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.4038 rms_B_bonded: 2.10
r_work: 0.3871 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3703 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7208
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4790  Z= 0.118
  Angle     :  0.524   5.381   6498  Z= 0.270
  Chirality :  0.040   0.147    761
  Planarity :  0.002   0.025    793
  Dihedral  :  4.999  53.960    699
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 21.61 %
    Favored  : 74.57 %
  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: -1.07 (0.36), residues: 571
  helix:  1.56 (0.36), residues: 213
  sheet: -1.71 (0.48), residues: 115
  loop : -2.34 (0.37), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG e 117 
 TYR   0.011   0.001   TYR n 263 
 PHE   0.009   0.001   PHE g  56 
 TRP   0.017   0.001   TRP d  43 
 HIS   0.002   0.001   HIS f  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 4781)
  covalent geometry    : angle       0.52141 ( 6480)
  SS BOND              : bond        0.00206 (    9)
  SS BOND              : angle       1.12556 (   18)
  hydrogen bonds       : bond        0.03378 (  212)
  hydrogen bonds       : angle       3.72535 (  597)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 53
  time to evaluate  : 0.165 
Fit side-chains
REVERT: a   30 LYS cc_start: 0.7041 (ptpt) cc_final: 0.6015 (tptp)
REVERT: a   45 ILE cc_start: 0.8430 (mt) cc_final: 0.8162 (mp)
REVERT: e  123 MET cc_start: 0.7333 (ptp) cc_final: 0.6880 (ptm)
REVERT: f   90 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7075 (mm)
REVERT: f  128 MET cc_start: 0.6187 (tpp) cc_final: 0.5313 (tpp)
REVERT: g   56 PHE cc_start: 0.7041 (m-10) cc_final: 0.6763 (m-10)
REVERT: g   71 LYS cc_start: 0.7616 (mttt) cc_final: 0.7255 (mttt)
REVERT: g   95 LYS cc_start: 0.8217 (mttt) cc_final: 0.7976 (tttt)
  outliers start: 20
  outliers final: 15
  residues processed: 68
  average time/residue: 0.0573
  time to fit residues: 5.1042
Evaluate side-chains
  69 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 53
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   27 LEU
Chi-restraints excluded: chain a residue   32 CYS
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain b residue   40 PHE
Chi-restraints excluded: chain b residue   46 LEU
Chi-restraints excluded: chain d residue   37 CYS
Chi-restraints excluded: chain d residue   68 ARG
Chi-restraints excluded: chain d residue  109 VAL
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue   98 CYS
Chi-restraints excluded: chain e residue  118 VAL
Chi-restraints excluded: chain e residue  119 CYS
Chi-restraints excluded: chain f residue   39 SER
Chi-restraints excluded: chain f residue   90 LEU
Chi-restraints excluded: chain n residue  252 THR
Chi-restraints excluded: chain n residue  257 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 27 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 42 optimal weight:    0.4980
   chunk 6 optimal weight:    4.9990
   chunk 50 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
e  81 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.225871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.180827 restraints weight = 4509.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.4050 rms_B_bonded: 2.10
r_work: 0.3888 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3724 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4790  Z= 0.112
  Angle     :  0.513   5.308   6498  Z= 0.266
  Chirality :  0.040   0.147    761
  Planarity :  0.002   0.025    793
  Dihedral  :  4.918  54.559    699
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 23.14 %
    Favored  : 73.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.90 (0.36), residues: 571
  helix:  1.69 (0.36), residues: 213
  sheet: -1.56 (0.48), residues: 115
  loop : -2.27 (0.37), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG d  63 
 TYR   0.011   0.001   TYR n 263 
 PHE   0.007   0.001   PHE m 288 
 TRP   0.017   0.001   TRP d  43 
 HIS   0.002   0.001   HIS f  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 4781)
  covalent geometry    : angle       0.51101 ( 6480)
  SS BOND              : bond        0.00211 (    9)
  SS BOND              : angle       1.04941 (   18)
  hydrogen bonds       : bond        0.03239 (  212)
  hydrogen bonds       : angle       3.60350 (  597)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 0.182 
Fit side-chains
REVERT: a   30 LYS cc_start: 0.7066 (ptpt) cc_final: 0.6125 (tptp)
REVERT: e  123 MET cc_start: 0.7329 (ptp) cc_final: 0.6879 (ptm)
REVERT: f  128 MET cc_start: 0.6208 (tpp) cc_final: 0.5342 (tpp)
REVERT: g   56 PHE cc_start: 0.7109 (m-10) cc_final: 0.6848 (m-10)
REVERT: g   71 LYS cc_start: 0.7732 (mttt) cc_final: 0.7348 (mttt)
REVERT: g   95 LYS cc_start: 0.8196 (mttt) cc_final: 0.7942 (tttt)
  outliers start: 17
  outliers final: 14
  residues processed: 66
  average time/residue: 0.0568
  time to fit residues: 4.9803
Evaluate side-chains
  68 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   27 LEU
Chi-restraints excluded: chain a residue   32 CYS
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain b residue   40 PHE
Chi-restraints excluded: chain b residue   46 LEU
Chi-restraints excluded: chain d residue   37 CYS
Chi-restraints excluded: chain d residue   68 ARG
Chi-restraints excluded: chain d residue  109 VAL
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue   98 CYS
Chi-restraints excluded: chain e residue  118 VAL
Chi-restraints excluded: chain e residue  119 CYS
Chi-restraints excluded: chain f residue  123 MET
Chi-restraints excluded: chain n residue  257 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 31 optimal weight:    7.9990
   chunk 0 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0370
   chunk 29 optimal weight:    0.0170
   chunk 44 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 4 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.5096

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

Flipped N/Q/H residues before XYZ refinement:
e  81 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.227207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.182674 restraints weight = 4531.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 2.07
r_work: 0.3899 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3733 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7182
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   4790  Z= 0.100
  Angle     :  0.491   5.531   6498  Z= 0.256
  Chirality :  0.039   0.144    761
  Planarity :  0.002   0.024    793
  Dihedral  :  4.785  54.342    699
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 23.90 %
    Favored  : 73.04 %
  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: -0.77 (0.36), residues: 571
  helix:  1.82 (0.36), residues: 213
  sheet: -1.49 (0.48), residues: 115
  loop : -2.22 (0.37), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG e 117 
 TYR   0.009   0.001   TYR n 263 
 PHE   0.006   0.001   PHE f  87 
 TRP   0.022   0.001   TRP d  43 
 HIS   0.002   0.001   HIS f  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 4781)
  covalent geometry    : angle       0.48938 ( 6480)
  SS BOND              : bond        0.00184 (    9)
  SS BOND              : angle       0.95384 (   18)
  hydrogen bonds       : bond        0.03026 (  212)
  hydrogen bonds       : angle       3.50707 (  597)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 53
  time to evaluate  : 0.133 
Fit side-chains
REVERT: a   30 LYS cc_start: 0.6838 (ptpt) cc_final: 0.6055 (tptp)
REVERT: e  123 MET cc_start: 0.7316 (ptp) cc_final: 0.6865 (ptm)
REVERT: f   90 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6963 (mm)
REVERT: f  128 MET cc_start: 0.6158 (tpp) cc_final: 0.5328 (tpp)
REVERT: g   56 PHE cc_start: 0.6999 (m-10) cc_final: 0.6771 (m-10)
REVERT: g   71 LYS cc_start: 0.7698 (mttt) cc_final: 0.7323 (mttt)
REVERT: g   95 LYS cc_start: 0.8156 (mttt) cc_final: 0.7887 (tttt)
  outliers start: 16
  outliers final: 11
  residues processed: 65
  average time/residue: 0.0607
  time to fit residues: 5.1028
Evaluate side-chains
  63 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   27 LEU
Chi-restraints excluded: chain a residue   32 CYS
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain b residue   40 PHE
Chi-restraints excluded: chain d residue   68 ARG
Chi-restraints excluded: chain d residue  109 VAL
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue   98 CYS
Chi-restraints excluded: chain e residue  119 CYS
Chi-restraints excluded: chain f residue   90 LEU
Chi-restraints excluded: chain n residue  252 THR
Chi-restraints excluded: chain n residue  257 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 7 optimal weight:    7.9990
   chunk 39 optimal weight:    0.0170
   chunk 37 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 22 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
e  81 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.226613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.181577 restraints weight = 4425.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.4045 rms_B_bonded: 2.10
r_work: 0.3870 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3700 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7194
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4790  Z= 0.109
  Angle     :  0.509   5.675   6498  Z= 0.264
  Chirality :  0.040   0.143    761
  Planarity :  0.002   0.023    793
  Dihedral  :  4.786  55.645    699
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 24.09 %
    Favored  : 72.66 %
  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: -0.75 (0.36), residues: 571
  helix:  1.83 (0.36), residues: 214
  sheet: -1.35 (0.49), residues: 109
  loop : -2.28 (0.37), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG d  72 
 TYR   0.011   0.001   TYR n 263 
 PHE   0.007   0.001   PHE m 288 
 TRP   0.023   0.001   TRP d  43 
 HIS   0.002   0.001   HIS f  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 4781)
  covalent geometry    : angle       0.50640 ( 6480)
  SS BOND              : bond        0.00205 (    9)
  SS BOND              : angle       1.01552 (   18)
  hydrogen bonds       : bond        0.03105 (  212)
  hydrogen bonds       : angle       3.43075 (  597)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 51
  time to evaluate  : 0.163 
Fit side-chains
REVERT: a   30 LYS cc_start: 0.6819 (ptpt) cc_final: 0.6028 (tptp)
REVERT: e  123 MET cc_start: 0.7281 (ptp) cc_final: 0.6853 (ptm)
REVERT: f   90 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6978 (mm)
REVERT: f  128 MET cc_start: 0.6282 (tpp) cc_final: 0.5401 (tpp)
REVERT: g   56 PHE cc_start: 0.7000 (m-10) cc_final: 0.6772 (m-10)
REVERT: g   71 LYS cc_start: 0.7633 (mttt) cc_final: 0.7279 (mttt)
REVERT: g   95 LYS cc_start: 0.8145 (mttt) cc_final: 0.7862 (tttt)
  outliers start: 17
  outliers final: 12
  residues processed: 66
  average time/residue: 0.0602
  time to fit residues: 5.2400
Evaluate side-chains
  64 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   27 LEU
Chi-restraints excluded: chain a residue   32 CYS
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain b residue   40 PHE
Chi-restraints excluded: chain b residue   46 LEU
Chi-restraints excluded: chain d residue   68 ARG
Chi-restraints excluded: chain d residue  109 VAL
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue   98 CYS
Chi-restraints excluded: chain e residue  119 CYS
Chi-restraints excluded: chain f residue   90 LEU
Chi-restraints excluded: chain n residue  252 THR
Chi-restraints excluded: chain n residue  257 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 12 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 44 optimal weight:    0.3980
   chunk 18 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
e  81 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.226880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.181220 restraints weight = 4509.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.4046 rms_B_bonded: 2.13
r_work: 0.3877 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3707 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7161
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   4790  Z= 0.107
  Angle     :  0.499   5.854   6498  Z= 0.260
  Chirality :  0.039   0.142    761
  Planarity :  0.002   0.023    793
  Dihedral  :  4.769  56.225    699
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 23.90 %
    Favored  : 73.23 %
  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: -0.65 (0.36), residues: 571
  helix:  1.92 (0.37), residues: 213
  sheet: -1.25 (0.50), residues: 109
  loop : -2.24 (0.36), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG e 117 
 TYR   0.010   0.001   TYR n 263 
 PHE   0.007   0.001   PHE m 288 
 TRP   0.022   0.001   TRP d  43 
 HIS   0.002   0.001   HIS f  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 4781)
  covalent geometry    : angle       0.49747 ( 6480)
  SS BOND              : bond        0.00190 (    9)
  SS BOND              : angle       0.94690 (   18)
  hydrogen bonds       : bond        0.03078 (  212)
  hydrogen bonds       : angle       3.37902 (  597)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.197 
Fit side-chains
REVERT: a   30 LYS cc_start: 0.6760 (ptpt) cc_final: 0.5981 (tptp)
REVERT: e  123 MET cc_start: 0.7320 (ptp) cc_final: 0.6904 (ptm)
REVERT: f   90 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.7009 (mm)
REVERT: f  128 MET cc_start: 0.6247 (tpp) cc_final: 0.5363 (tpp)
REVERT: g   56 PHE cc_start: 0.6948 (m-10) cc_final: 0.6732 (m-10)
REVERT: g   71 LYS cc_start: 0.7639 (mttt) cc_final: 0.7287 (mttt)
REVERT: g   95 LYS cc_start: 0.8143 (mttt) cc_final: 0.7827 (tttt)
  outliers start: 15
  outliers final: 13
  residues processed: 63
  average time/residue: 0.0817
  time to fit residues: 6.6873
Evaluate side-chains
  65 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   27 LEU
Chi-restraints excluded: chain a residue   32 CYS
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain b residue   40 PHE
Chi-restraints excluded: chain d residue   68 ARG
Chi-restraints excluded: chain d residue  109 VAL
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue   98 CYS
Chi-restraints excluded: chain e residue  118 VAL
Chi-restraints excluded: chain e residue  119 CYS
Chi-restraints excluded: chain f residue   48 THR
Chi-restraints excluded: chain f residue   90 LEU
Chi-restraints excluded: chain n residue  252 THR
Chi-restraints excluded: chain n residue  257 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 41 optimal weight:    0.0020
   chunk 44 optimal weight:    5.9990
   overall best weight:    0.9190

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

Flipped N/Q/H residues before XYZ refinement:
e  81 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.224179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.178566 restraints weight = 4513.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.4024 rms_B_bonded: 2.11
r_work: 0.3858 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3691 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.2278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4790  Z= 0.132
  Angle     :  0.534   5.531   6498  Z= 0.275
  Chirality :  0.040   0.146    761
  Planarity :  0.002   0.022    793
  Dihedral  :  4.946  58.766    699
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 24.28 %
    Favored  : 73.04 %
  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: -0.75 (0.36), residues: 571
  helix:  1.76 (0.36), residues: 213
  sheet: -1.23 (0.50), residues: 109
  loop : -2.26 (0.37), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG d  91 
 TYR   0.014   0.001   TYR n 263 
 PHE   0.008   0.001   PHE m 288 
 TRP   0.020   0.001   TRP d  43 
 HIS   0.002   0.001   HIS f  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 4781)
  covalent geometry    : angle       0.53240 ( 6480)
  SS BOND              : bond        0.00229 (    9)
  SS BOND              : angle       1.03419 (   18)
  hydrogen bonds       : bond        0.03414 (  212)
  hydrogen bonds       : angle       3.48342 (  597)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1298.06 seconds
wall clock time: 22 minutes 54.23 seconds (1374.23 seconds total)