Starting phenix.real_space_refine
on Wed Sep 17 12:34:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zz0_60585/09_2025/8zz0_60585.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zz0_60585/09_2025/8zz0_60585.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zz0_60585/09_2025/8zz0_60585.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zz0_60585/09_2025/8zz0_60585.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zz0_60585/09_2025/8zz0_60585.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zz0_60585/09_2025/8zz0_60585.map"
  }
  resolution = 3.43
  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=   0.013
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      78      5.16       5
     C    5745      2.51       5
     N    1471      2.21       5
     O    1620      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8914
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 361
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 361
          Classifications: {'peptide': 46}
          Link IDs: {'PTRANS': 1, 'TRANS': 44}
    Chain: "B"
      Number of atoms: 368
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 368
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 1, 'TRANS': 45}
    Chain: "C"
      Number of atoms: 1606
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 211, 1601
          Classifications: {'peptide': 211}
          Link IDs: {'PTRANS': 6, 'TRANS': 204}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 211, 1601
          Classifications: {'peptide': 211}
          Link IDs: {'PTRANS': 6, 'TRANS': 204}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1616
    Chain: "D"
      Number of atoms: 1621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1621
          Classifications: {'peptide': 214}
          Link IDs: {'PTRANS': 6, 'TRANS': 207}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1613
          Classifications: {'peptide': 213}
          Link IDs: {'PTRANS': 6, 'TRANS': 206}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1729
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1729
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 6, 'TRANS': 223}
          Chain breaks: 2
    Chain: "G"
      Number of atoms: 1613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1613
          Classifications: {'peptide': 213}
          Link IDs: {'PTRANS': 6, 'TRANS': 206}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "G"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" O   HOH G 301 " occ=0.68
  Time building chain proxies: 2.88, per 1000 atoms: 0.32
  Number of scatterers: 8914
  At special positions: 0
  Unit cell: (102.6, 98.55, 105.3, 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      78     16.00
     O    1620      8.00
     N    1471      7.00
     C    5745      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: 0.82
  Conformation dependent library (CDL) restraints added in 430.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2140

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 1 sheets defined
      91.8% alpha, 0.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 39
      removed outlier: 3.908A  pdb=" N   GLY A  20 " --> pdb=" O   PRO A  16 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   PHE A  39 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 59
    Processing helix  chain 'B' and resid 18 through 39
      removed outlier: 4.005A  pdb=" N   PHE B  39 " --> pdb=" O   LEU B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 58
    Processing helix  chain 'C' and resid 31 through 50
      removed outlier: 3.528A  pdb=" N   ILE C  35 " --> pdb=" O   ASP C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 68
    Processing helix  chain 'C' and resid 72 through 87
    Processing helix  chain 'C' and resid 102 through 114
      removed outlier: 3.602A  pdb=" N   ASP C 114 " --> pdb=" O   ASP C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 168
      removed outlier: 3.543A  pdb=" N   VAL C 121 " --> pdb=" O   ASP C 117 " (cutoff:3.500A)
      Proline residue:  C 151  - end of helix
    Processing helix  chain 'C' and resid 171 through 173
      No H-bonds generated for 'chain 'C' and resid 171 through 173'
    Processing helix  chain 'C' and resid 174 through 195
      removed outlier: 3.928A  pdb=" N   MET C 179 " --> pdb=" O   ILE C 175 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL C 181 " --> pdb=" O   PRO C 177 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ALA C 182 " --> pdb=" O   ALA C 178 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   THR C 185 " --> pdb=" O   VAL C 181 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   THR C 186 " --> pdb=" O   ALA C 182 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 228
    Processing helix  chain 'C' and resid 230 through 240
      removed outlier: 3.540A  pdb=" N   ILE C 234 " --> pdb=" O   ASN C 230 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 241 through 244
      removed outlier: 3.605A  pdb=" N   GLU C 244 " --> pdb=" O   TYR C 241 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 241 through 244'
    Processing helix  chain 'D' and resid 26 through 30
    Processing helix  chain 'D' and resid 31 through 48
      removed outlier: 3.792A  pdb=" N   MET D  48 " --> pdb=" O   PHE D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 68
    Processing helix  chain 'D' and resid 72 through 87
      removed outlier: 3.744A  pdb=" N   ASP D  85 " --> pdb=" O   VAL D  81 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   ALA D  86 " --> pdb=" O   GLU D  82 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ALA D  87 " --> pdb=" O   MET D  83 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 102 through 115
    Processing helix  chain 'D' and resid 117 through 168
      Proline residue:  D 151  - end of helix
      removed outlier: 3.666A  pdb=" N   ASN D 168 " --> pdb=" O   ALA D 164 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 175 through 195
      removed outlier: 4.306A  pdb=" N   ALA D 182 " --> pdb=" O   ALA D 178 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 196 through 228
    Processing helix  chain 'D' and resid 232 through 239
      removed outlier: 3.657A  pdb=" N   SER D 236 " --> pdb=" O   ARG D 232 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   TYR D 237 " --> pdb=" O   VAL D 233 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   LYS D 239 " --> pdb=" O   ASP D 235 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 244 through 250
      removed outlier: 3.841A  pdb=" N   ARG D 247 " --> pdb=" O   GLU D 244 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LEU D 249 " --> pdb=" O   LYS D 246 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 27 through 48
      removed outlier: 3.661A  pdb=" N   ASP E  31 " --> pdb=" O   GLY E  27 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 68
    Processing helix  chain 'E' and resid 72 through 87
      removed outlier: 3.827A  pdb=" N   LEU E  76 " --> pdb=" O   GLU E  72 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 102 through 114
    Processing helix  chain 'E' and resid 117 through 168
      Proline residue:  E 151  - end of helix
    Processing helix  chain 'E' and resid 171 through 196
      removed outlier: 3.852A  pdb=" N   GLY E 176 " --> pdb=" O   PRO E 172 " (cutoff:3.500A)
      Proline residue:  E 177  - end of helix
      removed outlier: 3.599A  pdb=" N   VAL E 196 " --> pdb=" O   LEU E 192 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 196 through 228
    Processing helix  chain 'E' and resid 230 through 241
      removed outlier: 3.695A  pdb=" N   TYR E 241 " --> pdb=" O   TYR E 237 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 242 through 248
      removed outlier: 6.739A  pdb=" N   GLY E 245 " --> pdb=" O   LEU E 242 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   LYS E 246 " --> pdb=" O   ASN E 243 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ARG E 247 " --> pdb=" O   GLU E 244 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   ALA E 248 " --> pdb=" O   GLY E 245 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 242 through 248'
    Processing helix  chain 'F' and resid 4 through 23
    Processing helix  chain 'F' and resid 32 through 47
    Processing helix  chain 'F' and resid 51 through 68
    Processing helix  chain 'F' and resid 72 through 87
    Processing helix  chain 'F' and resid 103 through 115
      removed outlier: 3.681A  pdb=" N   GLY F 115 " --> pdb=" O   LEU F 111 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 117 through 168
      Proline residue:  F 151  - end of helix
    Processing helix  chain 'F' and resid 171 through 173
      No H-bonds generated for 'chain 'F' and resid 171 through 173'
    Processing helix  chain 'F' and resid 174 through 195
      removed outlier: 3.634A  pdb=" N   THR F 185 " --> pdb=" O   VAL F 181 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   THR F 186 " --> pdb=" O   ALA F 182 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 196 through 228
    Processing helix  chain 'F' and resid 230 through 243
    Processing helix  chain 'F' and resid 244 through 251
      removed outlier: 4.113A  pdb=" N   ARG F 247 " --> pdb=" O   GLU F 244 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU F 249 " --> pdb=" O   LYS F 246 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ILE F 251 " --> pdb=" O   ALA F 248 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 28 through 50
    Processing helix  chain 'G' and resid 51 through 67
    Processing helix  chain 'G' and resid 72 through 87
      removed outlier: 3.769A  pdb=" N   LEU G  76 " --> pdb=" O   GLU G  72 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 102 through 115
    Processing helix  chain 'G' and resid 117 through 169
      removed outlier: 3.829A  pdb=" N   VAL G 121 " --> pdb=" O   ASP G 117 " (cutoff:3.500A)
      Proline residue:  G 151  - end of helix
    Processing helix  chain 'G' and resid 171 through 195
      removed outlier: 3.529A  pdb=" N   GLY G 176 " --> pdb=" O   PRO G 172 " (cutoff:3.500A)
      Proline residue:  G 177  - end of helix
    Processing helix  chain 'G' and resid 196 through 228
    Processing helix  chain 'G' and resid 230 through 243
      removed outlier: 3.521A  pdb=" N   LYS G 239 " --> pdb=" O   ASP G 235 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   ASN G 240 " --> pdb=" O   SER G 236 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   TYR G 241 " --> pdb=" O   TYR G 237 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ASN G 243 " --> pdb=" O   LYS G 239 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 244 through 249
      removed outlier: 3.934A  pdb=" N   ARG G 247 " --> pdb=" O   GLU G 244 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42

    808 hydrogen bonds defined for protein.
    2399 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.64

  Time building geometry restraints manager: 1.04 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2896
        1.35 -     1.47: 1892
        1.47 -     1.58: 4093
        1.58 -     1.70: 0
        1.70 -     1.82: 154
  Bond restraints: 9035
  Sorted by residual:
  bond pdb=" CB  PRO G 172 "
       pdb=" CG  PRO G 172 "
    ideal  model  delta    sigma   weight residual
    1.492  1.568 -0.076 5.00e-02 4.00e+02 2.30e+00
  bond pdb=" CB  ASP F 227 "
       pdb=" CG  ASP F 227 "
    ideal  model  delta    sigma   weight residual
    1.516  1.553 -0.037 2.50e-02 1.60e+03 2.19e+00
  bond pdb=" CA  ASP C 171 "
       pdb=" CB  ASP C 171 "
    ideal  model  delta    sigma   weight residual
    1.530  1.550 -0.020 1.38e-02 5.25e+03 2.15e+00
  bond pdb=" CA  ASP F 170 "
       pdb=" CB  ASP F 170 "
    ideal  model  delta    sigma   weight residual
    1.534  1.557 -0.023 1.55e-02 4.16e+03 2.15e+00
  bond pdb=" CA  ASP F 227 "
       pdb=" CB  ASP F 227 "
    ideal  model  delta    sigma   weight residual
    1.530  1.553 -0.023 1.68e-02 3.54e+03 1.89e+00
  ... (remaining 9030 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 12014
        2.00 -     4.00: 116
        4.00 -     6.00: 32
        6.00 -     8.01: 6
        8.01 -    10.01: 1
  Bond angle restraints: 12169
  Sorted by residual:
  angle pdb=" CB  LYS B  48 "
        pdb=" CG  LYS B  48 "
        pdb=" CD  LYS B  48 "
      ideal   model   delta    sigma   weight residual
     111.30  118.38   -7.08 2.30e+00 1.89e-01 9.48e+00
  angle pdb=" CA  PRO E 172 "
        pdb=" N   PRO E 172 "
        pdb=" CD  PRO E 172 "
      ideal   model   delta    sigma   weight residual
     112.00  107.80    4.20 1.40e+00 5.10e-01 9.00e+00
  angle pdb=" CA  LEU F 112 "
        pdb=" CB  LEU F 112 "
        pdb=" CG  LEU F 112 "
      ideal   model   delta    sigma   weight residual
     116.30  126.31  -10.01 3.50e+00 8.16e-02 8.18e+00
  angle pdb=" CA  ASP F 227 "
        pdb=" CB  ASP F 227 "
        pdb=" CG  ASP F 227 "
      ideal   model   delta    sigma   weight residual
     112.60  115.46   -2.86 1.00e+00 1.00e+00 8.16e+00
  angle pdb=" CG  ARG E 216 "
        pdb=" CD  ARG E 216 "
        pdb=" NE  ARG E 216 "
      ideal   model   delta    sigma   weight residual
     112.00  117.90   -5.90 2.20e+00 2.07e-01 7.20e+00
  ... (remaining 12164 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.18: 4617
       18.18 -    36.35: 627
       36.35 -    54.53: 179
       54.53 -    72.70: 20
       72.70 -    90.88: 7
  Dihedral angle restraints: 5450
    sinusoidal: 2132
      harmonic: 3318
  Sorted by residual:
  dihedral pdb=" CB  GLU D  72 "
           pdb=" CG  GLU D  72 "
           pdb=" CD  GLU D  72 "
           pdb=" OE1 GLU D  72 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   90.88  -90.88     1      3.00e+01 1.11e-03 1.08e+01
  dihedral pdb=" CA  ASN G 243 "
           pdb=" CB  ASN G 243 "
           pdb=" CG  ASN G 243 "
           pdb=" OD1 ASN G 243 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -169.82  -70.18     2      2.00e+01 2.50e-03 1.06e+01
  dihedral pdb=" CA  ASP E  85 "
           pdb=" CB  ASP E  85 "
           pdb=" CG  ASP E  85 "
           pdb=" OD1 ASP E  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.40   54.40     1      2.00e+01 2.50e-03 1.00e+01
  ... (remaining 5447 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1193
       0.050 -    0.099: 226
       0.099 -    0.148: 27
       0.148 -    0.198: 0
       0.198 -    0.247: 1
  Chirality restraints: 1447
  Sorted by residual:
  chirality pdb=" CB  VAL D  39 "
            pdb=" CA  VAL D  39 "
            pdb=" CG1 VAL D  39 "
            pdb=" CG2 VAL D  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.53e+00
  chirality pdb=" CG  LEU F 112 "
            pdb=" CB  LEU F 112 "
            pdb=" CD1 LEU F 112 "
            pdb=" CD2 LEU F 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.73    0.14 2.00e-01 2.50e+01 4.72e-01
  chirality pdb=" CA  PRO G  73 "
            pdb=" N   PRO G  73 "
            pdb=" C   PRO G  73 "
            pdb=" CB  PRO G  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.12 2.00e-01 2.50e+01 3.88e-01
  ... (remaining 1444 not shown)

  Planarity restraints: 1544
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E 171 "    0.067 5.00e-02 4.00e+02   1.00e-01 1.61e+01
        pdb=" N   PRO E 172 "   -0.174 5.00e-02 4.00e+02
        pdb=" CA  PRO E 172 "    0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO E 172 "    0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G 171 "   -0.064 5.00e-02 4.00e+02   9.63e-02 1.49e+01
        pdb=" N   PRO G 172 "    0.167 5.00e-02 4.00e+02
        pdb=" CA  PRO G 172 "   -0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO G 172 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP F 227 "   -0.011 2.00e-02 2.50e+03   2.26e-02 5.10e+00
        pdb=" C   ASP F 227 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ASP F 227 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   GLY F 228 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1541 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 84
        2.68 -     3.23: 8961
        3.23 -     3.79: 14453
        3.79 -     4.34: 17960
        4.34 -     4.90: 30596
  Nonbonded interactions: 72054
  Sorted by model distance:
  nonbonded pdb=" OG1 THR E 158 "
            pdb=" OG1 THR E 186 "
     model   vdw
     2.123 3.040
  nonbonded pdb=" O   PHE D  29 "
            pdb=" OH  TYR D 188 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" O   LEU B  45 "
            pdb=" NE2 GLN B  49 "
     model   vdw
     2.181 3.120
  nonbonded pdb=" N   GLU E  72 "
            pdb=" OE1 GLU E  72 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" OE2 GLU C  74 "
            pdb=" NH2 ARG C 247 "
     model   vdw
     2.276 3.120
  ... (remaining 72049 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and resid 14 through 59)
}
ncs_group {
  reference = (chain 'C' and (resid 29 through 154 or resid 156 through 250))
  selection = (chain 'D' and (resid 29 through 154 or resid 156 through 250))
  selection = (chain 'E' and (resid 29 through 154 or resid 156 through 250))
  selection = (chain 'F' and (resid 15 through 16 or resid 31 through 154 or resid 156 through \ 
 250))
  selection = (chain 'G' and (resid 29 through 154 or resid 156 through 250))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.44 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.680
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
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   0.076   9035  Z= 0.136
  Angle     :  0.582  10.008  12169  Z= 0.309
  Chirality :  0.037   0.247   1447
  Planarity :  0.005   0.100   1544
  Dihedral  : 17.581  90.879   3310
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 25.82 %
    Favored  : 74.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.96 (0.25), residues: 1149
  helix:  2.36 (0.17), residues: 987
  sheet:  None (None), residues: 0
  loop : -0.67 (0.50), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 135 
 TYR   0.016   0.001   TYR E 237 
 PHE   0.018   0.001   PHE G  44 
 TRP   0.007   0.001   TRP A  18 
 HIS   0.008   0.001   HIS E 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9035)
  covalent geometry    : angle       0.58233 (12169)
  hydrogen bonds       : bond        0.10864 (  808)
  hydrogen bonds       : angle       4.94612 ( 2399)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
REVERT: E  169 MET cc_start: 0.8074 (tpp) cc_final: 0.7377 (ttm)
REVERT: F   20 MET cc_start: 0.2868 (ptm) cc_final: 0.1922 (tpt)
REVERT: F  105 MET cc_start: 0.8202 (tpt) cc_final: 0.7676 (ttp)
REVERT: F  173 LYS cc_start: 0.7481 (mmtt) cc_final: 0.7276 (tttm)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.1101
  time to fit residues: 26.6914
Evaluate side-chains
  172 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    0.7980
   chunk 113 optimal weight:    0.2980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0270
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    6.9990
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
B  49 GLN
C 243 ASN
E 168 ASN
E 226 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.191083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.147308 restraints weight = 20685.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 2.55
r_work: 0.3155 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3068
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3068 r_free = 0.3068    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3068 r_free = 0.3068    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3068
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.0875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9035  Z= 0.113
  Angle     :  0.484   7.116  12169  Z= 0.251
  Chirality :  0.037   0.157   1447
  Planarity :  0.004   0.066   1544
  Dihedral  :  3.424  14.006   1223
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 23.38 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.48 (0.25), residues: 1149
  helix:  2.68 (0.16), residues: 1002
  sheet:  None (None), residues: 0
  loop : -0.61 (0.53), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 215 
 TYR   0.009   0.001   TYR E 237 
 PHE   0.017   0.001   PHE G  44 
 TRP   0.005   0.001   TRP A  18 
 HIS   0.006   0.001   HIS E 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 9035)
  covalent geometry    : angle       0.48399 (12169)
  hydrogen bonds       : bond        0.03756 (  808)
  hydrogen bonds       : angle       3.65534 ( 2399)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 186
  time to evaluate  : 0.319 
Fit side-chains
REVERT: C  219 MET cc_start: 0.6371 (ttp) cc_final: 0.5888 (ttt)
REVERT: E  169 MET cc_start: 0.8218 (tpp) cc_final: 0.7839 (ttm)
REVERT: E  220 ASP cc_start: 0.6609 (m-30) cc_final: 0.6109 (t70)
REVERT: F   20 MET cc_start: 0.2444 (ptm) cc_final: 0.1453 (tpt)
REVERT: F  105 MET cc_start: 0.8148 (tpt) cc_final: 0.7616 (ttp)
REVERT: F  119 ASP cc_start: 0.5225 (m-30) cc_final: 0.4958 (m-30)
REVERT: F  173 LYS cc_start: 0.7621 (mmtt) cc_final: 0.7171 (tttm)
  outliers start: 16
  outliers final: 11
  residues processed: 193
  average time/residue: 0.1022
  time to fit residues: 26.7258
Evaluate side-chains
  189 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 178
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue  208 ARG
Chi-restraints excluded: chain E residue  103 THR
Chi-restraints excluded: chain E residue  105 MET
Chi-restraints excluded: chain F residue  103 THR
Chi-restraints excluded: chain F residue  155 MET
Chi-restraints excluded: chain F residue  179 MET
Chi-restraints excluded: chain F residue  242 LEU
Chi-restraints excluded: chain G residue   35 ILE
Chi-restraints excluded: chain G residue  155 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 19 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 13 optimal weight:    8.9990
   chunk 33 optimal weight:    0.0770
   chunk 59 optimal weight:    9.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.7540

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

Flipped N/Q/H residues before XYZ refinement:
C 243 ASN
E 116 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.190089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.148872 restraints weight = 9826.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 2.05
r_work: 0.3144 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3055
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3055 r_free = 0.3055    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3055 r_free = 0.3055    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3055
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9035  Z= 0.111
  Angle     :  0.460   7.517  12169  Z= 0.239
  Chirality :  0.036   0.138   1447
  Planarity :  0.004   0.053   1544
  Dihedral  :  3.352  13.499   1223
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 23.17 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.66 (0.25), residues: 1149
  helix:  2.80 (0.16), residues: 1005
  sheet:  None (None), residues: 0
  loop : -0.57 (0.52), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 247 
 TYR   0.006   0.001   TYR D 188 
 PHE   0.012   0.001   PHE E 143 
 TRP   0.005   0.001   TRP A  18 
 HIS   0.002   0.001   HIS D 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 9035)
  covalent geometry    : angle       0.45972 (12169)
  hydrogen bonds       : bond        0.03646 (  808)
  hydrogen bonds       : angle       3.51932 ( 2399)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 191
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
REVERT: C  219 MET cc_start: 0.6374 (ttp) cc_final: 0.5827 (ttt)
REVERT: D  207 ARG cc_start: 0.8916 (tpt-90) cc_final: 0.8679 (tpp80)
REVERT: E  169 MET cc_start: 0.8363 (tpp) cc_final: 0.8106 (ttm)
REVERT: E  249 LEU cc_start: 0.7779 (pt) cc_final: 0.7461 (pp)
REVERT: F   20 MET cc_start: 0.2413 (ptm) cc_final: 0.1452 (tpt)
REVERT: F  105 MET cc_start: 0.8101 (tpt) cc_final: 0.7576 (ttp)
REVERT: F  119 ASP cc_start: 0.5248 (m-30) cc_final: 0.4969 (m-30)
  outliers start: 18
  outliers final: 10
  residues processed: 199
  average time/residue: 0.1028
  time to fit residues: 27.7322
Evaluate side-chains
  189 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 179
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue  208 ARG
Chi-restraints excluded: chain D residue   28 MET
Chi-restraints excluded: chain D residue   51 THR
Chi-restraints excluded: chain E residue   49 LYS
Chi-restraints excluded: chain E residue  103 THR
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain F residue  103 THR
Chi-restraints excluded: chain F residue  155 MET
Chi-restraints excluded: chain G residue  155 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 95 optimal weight:    0.7980
   chunk 35 optimal weight:    9.9990
   chunk 55 optimal weight:    9.9990
   chunk 67 optimal weight:    2.9990
   chunk 63 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 114 optimal weight:    7.9990
   chunk 69 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
C 243 ASN
D 106 GLN
E 116 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.178711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 106)---------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.121278 restraints weight = 13619.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 2.34
r_work: 0.3085 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3049
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3049 r_free = 0.3049    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3049 r_free = 0.3049    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3049
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.1443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9035  Z= 0.136
  Angle     :  0.488   8.848  12169  Z= 0.252
  Chirality :  0.037   0.153   1447
  Planarity :  0.004   0.049   1544
  Dihedral  :  3.408  13.380   1223
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 23.38 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  3.62 (0.24), residues: 1149
  helix:  2.77 (0.16), residues: 1005
  sheet:  None (None), residues: 0
  loop : -0.61 (0.51), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 216 
 TYR   0.007   0.001   TYR E 237 
 PHE   0.013   0.001   PHE E 143 
 TRP   0.004   0.001   TRP A  18 
 HIS   0.004   0.001   HIS D 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 9035)
  covalent geometry    : angle       0.48810 (12169)
  hydrogen bonds       : bond        0.03807 (  808)
  hydrogen bonds       : angle       3.53150 ( 2399)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 186
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 MET cc_start: 0.8196 (ttp) cc_final: 0.7782 (ttp)
REVERT: B   49 GLN cc_start: 0.7430 (mt0) cc_final: 0.6859 (mt0)
REVERT: C  219 MET cc_start: 0.6567 (ttp) cc_final: 0.5958 (ttt)
REVERT: C  247 ARG cc_start: 0.7746 (ptm160) cc_final: 0.7520 (ptm160)
REVERT: D  207 ARG cc_start: 0.8947 (tpt-90) cc_final: 0.8696 (tpp80)
REVERT: E  169 MET cc_start: 0.8212 (tpp) cc_final: 0.7953 (ttm)
REVERT: E  249 LEU cc_start: 0.7675 (pt) cc_final: 0.7353 (pp)
REVERT: F   20 MET cc_start: 0.2459 (ptm) cc_final: 0.1602 (tpt)
REVERT: F   46 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8377 (t)
REVERT: F   69 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7776 (mttt)
REVERT: F  105 MET cc_start: 0.8185 (tpt) cc_final: 0.7693 (ttp)
REVERT: F  135 ARG cc_start: 0.8603 (ttm-80) cc_final: 0.8375 (ttp-170)
  outliers start: 21
  outliers final: 13
  residues processed: 196
  average time/residue: 0.0997
  time to fit residues: 26.3336
Evaluate side-chains
  193 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 179
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue  208 ARG
Chi-restraints excluded: chain D residue   51 THR
Chi-restraints excluded: chain E residue   49 LYS
Chi-restraints excluded: chain E residue   67 MET
Chi-restraints excluded: chain E residue  103 THR
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain F residue   36 LEU
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain F residue  103 THR
Chi-restraints excluded: chain F residue  155 MET
Chi-restraints excluded: chain F residue  179 MET
Chi-restraints excluded: chain G residue   35 ILE
Chi-restraints excluded: chain G residue  155 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 88 optimal weight:    0.7980
   chunk 89 optimal weight:    0.8980
   chunk 112 optimal weight:    9.9990
   chunk 22 optimal weight:    0.6980
   chunk 104 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   chunk 73 optimal weight:    4.9990
   chunk 107 optimal weight:    3.9990
   chunk 101 optimal weight:    9.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
C 243 ASN
E 116 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.187134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.128480 restraints weight = 13626.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 2.06
r_work: 0.3049 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3020
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3020 r_free = 0.3020    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3020 r_free = 0.3020    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3020
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9035  Z= 0.120
  Angle     :  0.471   7.516  12169  Z= 0.243
  Chirality :  0.036   0.160   1447
  Planarity :  0.004   0.045   1544
  Dihedral  :  3.400  13.830   1223
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 23.80 %
    Favored  : 73.96 %
  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:  3.68 (0.24), residues: 1149
  helix:  2.83 (0.16), residues: 1005
  sheet:  None (None), residues: 0
  loop : -0.68 (0.51), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 216 
 TYR   0.012   0.001   TYR E 237 
 PHE   0.013   0.001   PHE E 143 
 TRP   0.006   0.001   TRP A  18 
 HIS   0.003   0.001   HIS D 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 9035)
  covalent geometry    : angle       0.47074 (12169)
  hydrogen bonds       : bond        0.03629 (  808)
  hydrogen bonds       : angle       3.48336 ( 2399)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 193
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 MET cc_start: 0.8096 (ttp) cc_final: 0.7703 (tmm)
REVERT: C  179 MET cc_start: 0.7962 (ptm) cc_final: 0.7693 (ttt)
REVERT: C  219 MET cc_start: 0.6717 (ttp) cc_final: 0.6106 (ttt)
REVERT: C  247 ARG cc_start: 0.7716 (ptm160) cc_final: 0.7502 (ptm160)
REVERT: D  207 ARG cc_start: 0.8958 (tpt-90) cc_final: 0.8716 (tpp80)
REVERT: D  208 ARG cc_start: 0.8239 (ttp80) cc_final: 0.7916 (ttp-170)
REVERT: E  169 MET cc_start: 0.8178 (tpp) cc_final: 0.7968 (ttm)
REVERT: E  249 LEU cc_start: 0.7791 (pt) cc_final: 0.7426 (pp)
REVERT: F   20 MET cc_start: 0.2184 (ptm) cc_final: 0.1445 (tpt)
REVERT: F   69 LYS cc_start: 0.8127 (ttmt) cc_final: 0.7791 (mttt)
REVERT: F  105 MET cc_start: 0.8201 (tpt) cc_final: 0.7689 (ttp)
REVERT: F  135 ARG cc_start: 0.8648 (ttm-80) cc_final: 0.8433 (ttp-170)
REVERT: F  235 ASP cc_start: 0.6768 (m-30) cc_final: 0.6163 (t0)
  outliers start: 21
  outliers final: 15
  residues processed: 204
  average time/residue: 0.1128
  time to fit residues: 30.6503
Evaluate side-chains
  196 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 181
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue  208 ARG
Chi-restraints excluded: chain D residue   51 THR
Chi-restraints excluded: chain E residue   49 LYS
Chi-restraints excluded: chain E residue  103 THR
Chi-restraints excluded: chain E residue  105 MET
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain F residue   36 LEU
Chi-restraints excluded: chain F residue   49 LYS
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue  103 THR
Chi-restraints excluded: chain F residue  155 MET
Chi-restraints excluded: chain F residue  179 MET
Chi-restraints excluded: chain G residue   35 ILE
Chi-restraints excluded: chain G residue  155 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 109 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 89 optimal weight:    4.9990
   chunk 95 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 48 optimal weight:    7.9990
   chunk 0 optimal weight:    5.9990
   chunk 80 optimal weight:    9.9990
   chunk 66 optimal weight:    0.5980
   chunk 94 optimal weight:    3.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
E 116 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.184190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.128487 restraints weight = 11845.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 2.12
r_work: 0.3093 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3062
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3062
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9035  Z= 0.129
  Angle     :  0.490   6.973  12169  Z= 0.253
  Chirality :  0.037   0.190   1447
  Planarity :  0.004   0.042   1544
  Dihedral  :  3.442  13.777   1223
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 24.34 %
    Favored  : 73.43 %
  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:  3.59 (0.24), residues: 1149
  helix:  2.78 (0.16), residues: 1005
  sheet:  None (None), residues: 0
  loop : -0.80 (0.50), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG E 232 
 TYR   0.018   0.001   TYR E 237 
 PHE   0.013   0.001   PHE E 143 
 TRP   0.005   0.001   TRP A  18 
 HIS   0.003   0.001   HIS D 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 9035)
  covalent geometry    : angle       0.48952 (12169)
  hydrogen bonds       : bond        0.03720 (  808)
  hydrogen bonds       : angle       3.49826 ( 2399)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 186
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 MET cc_start: 0.8195 (ttp) cc_final: 0.7867 (tmm)
REVERT: C  179 MET cc_start: 0.7853 (ptm) cc_final: 0.7553 (ttt)
REVERT: C  219 MET cc_start: 0.6462 (ttp) cc_final: 0.5805 (ttt)
REVERT: C  247 ARG cc_start: 0.7667 (ptm160) cc_final: 0.7431 (ptm160)
REVERT: D  207 ARG cc_start: 0.8917 (tpt-90) cc_final: 0.8668 (tpp80)
REVERT: D  208 ARG cc_start: 0.8236 (ttp80) cc_final: 0.7875 (ttp-170)
REVERT: E  169 MET cc_start: 0.8153 (tpp) cc_final: 0.7922 (ttm)
REVERT: E  249 LEU cc_start: 0.7735 (pt) cc_final: 0.7401 (pp)
REVERT: F   20 MET cc_start: 0.2414 (ptm) cc_final: 0.1657 (tpt)
REVERT: F   69 LYS cc_start: 0.8091 (ttmt) cc_final: 0.7774 (mttt)
REVERT: F  105 MET cc_start: 0.8271 (tpt) cc_final: 0.7724 (ttp)
REVERT: F  135 ARG cc_start: 0.8531 (ttm-80) cc_final: 0.8309 (ttp-170)
REVERT: F  235 ASP cc_start: 0.6695 (m-30) cc_final: 0.6149 (t0)
  outliers start: 21
  outliers final: 16
  residues processed: 195
  average time/residue: 0.1045
  time to fit residues: 27.4123
Evaluate side-chains
  197 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 181
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue  208 ARG
Chi-restraints excluded: chain D residue   51 THR
Chi-restraints excluded: chain E residue   49 LYS
Chi-restraints excluded: chain E residue   67 MET
Chi-restraints excluded: chain E residue  103 THR
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain F residue   36 LEU
Chi-restraints excluded: chain F residue   49 LYS
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue  103 THR
Chi-restraints excluded: chain F residue  112 LEU
Chi-restraints excluded: chain F residue  155 MET
Chi-restraints excluded: chain F residue  179 MET
Chi-restraints excluded: chain G residue   35 ILE
Chi-restraints excluded: chain G residue  155 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 91 optimal weight:    8.9990
   chunk 93 optimal weight:    6.9990
   chunk 68 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 58 optimal weight:    9.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
E 116 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.181255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.124484 restraints weight = 17379.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 2.32
r_work: 0.2964 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2929
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2929
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.2038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9035  Z= 0.169
  Angle     :  0.524   6.799  12169  Z= 0.272
  Chirality :  0.039   0.203   1447
  Planarity :  0.004   0.042   1544
  Dihedral  :  3.581  13.624   1223
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 24.87 %
    Favored  : 72.69 %
  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:  3.33 (0.25), residues: 1149
  helix:  2.58 (0.16), residues: 1010
  sheet:  None (None), residues: 0
  loop : -0.82 (0.51), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 216 
 TYR   0.015   0.001   TYR E 237 
 PHE   0.016   0.002   PHE F 143 
 TRP   0.004   0.001   TRP A  18 
 HIS   0.005   0.001   HIS D 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 9035)
  covalent geometry    : angle       0.52392 (12169)
  hydrogen bonds       : bond        0.04075 (  808)
  hydrogen bonds       : angle       3.59794 ( 2399)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 186
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8099 (mp)
REVERT: C  148 ASP cc_start: 0.8051 (m-30) cc_final: 0.7795 (m-30)
REVERT: C  219 MET cc_start: 0.6570 (ttp) cc_final: 0.6052 (ttt)
REVERT: C  247 ARG cc_start: 0.7626 (ptm160) cc_final: 0.7356 (ptm160)
REVERT: D  207 ARG cc_start: 0.9040 (tpt-90) cc_final: 0.8801 (tpp80)
REVERT: D  208 ARG cc_start: 0.8370 (ttp80) cc_final: 0.8054 (ttp-170)
REVERT: E  128 ASP cc_start: 0.7932 (t0) cc_final: 0.7092 (t0)
REVERT: F   20 MET cc_start: 0.2567 (ptm) cc_final: 0.1667 (tpt)
REVERT: F  105 MET cc_start: 0.8191 (tpt) cc_final: 0.7750 (ttp)
REVERT: F  135 ARG cc_start: 0.8756 (ttm-80) cc_final: 0.8452 (ttp-170)
REVERT: F  235 ASP cc_start: 0.6845 (m-30) cc_final: 0.6352 (t0)
REVERT: G   56 PHE cc_start: 0.8855 (m-80) cc_final: 0.8378 (m-80)
  outliers start: 23
  outliers final: 17
  residues processed: 198
  average time/residue: 0.1109
  time to fit residues: 29.1161
Evaluate side-chains
  199 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 181
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue  158 THR
Chi-restraints excluded: chain C residue  208 ARG
Chi-restraints excluded: chain D residue   51 THR
Chi-restraints excluded: chain E residue   49 LYS
Chi-restraints excluded: chain E residue   67 MET
Chi-restraints excluded: chain E residue  103 THR
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain F residue   49 LYS
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue  103 THR
Chi-restraints excluded: chain F residue  155 MET
Chi-restraints excluded: chain F residue  179 MET
Chi-restraints excluded: chain G residue   35 ILE
Chi-restraints excluded: chain G residue  155 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 99 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 87 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.4064 r_free = 0.4064 target = 0.186710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 134)---------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.130076 restraints weight = 15912.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 2.37
r_work: 0.3032 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3000
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3000
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9035  Z= 0.127
  Angle     :  0.494   7.243  12169  Z= 0.256
  Chirality :  0.037   0.202   1447
  Planarity :  0.004   0.041   1544
  Dihedral  :  3.500  13.554   1223
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 24.65 %
    Favored  : 73.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  3.53 (0.25), residues: 1149
  helix:  2.74 (0.16), residues: 999
  sheet:  None (None), residues: 0
  loop : -0.70 (0.49), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 216 
 TYR   0.012   0.001   TYR E 237 
 PHE   0.014   0.001   PHE E 143 
 TRP   0.006   0.001   TRP A  18 
 HIS   0.006   0.001   HIS E 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 9035)
  covalent geometry    : angle       0.49355 (12169)
  hydrogen bonds       : bond        0.03719 (  808)
  hydrogen bonds       : angle       3.51899 ( 2399)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 190
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 MET cc_start: 0.8210 (ttp) cc_final: 0.7872 (ttp)
REVERT: C   36 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8064 (mp)
REVERT: C  148 ASP cc_start: 0.7922 (m-30) cc_final: 0.7696 (m-30)
REVERT: C  179 MET cc_start: 0.8031 (ptm) cc_final: 0.7772 (ttt)
REVERT: C  219 MET cc_start: 0.6616 (ttp) cc_final: 0.6226 (ttt)
REVERT: C  247 ARG cc_start: 0.7563 (ptm160) cc_final: 0.7321 (ptm160)
REVERT: D  207 ARG cc_start: 0.8977 (tpt-90) cc_final: 0.8737 (tpp80)
REVERT: D  208 ARG cc_start: 0.8335 (ttp80) cc_final: 0.8027 (ttp-170)
REVERT: E   72 GLU cc_start: 0.7503 (pm20) cc_final: 0.6791 (tt0)
REVERT: E   74 GLU cc_start: 0.7818 (mp0) cc_final: 0.7332 (mp0)
REVERT: E  128 ASP cc_start: 0.7855 (t0) cc_final: 0.7025 (t0)
REVERT: F   20 MET cc_start: 0.2518 (ptm) cc_final: 0.1799 (tpt)
REVERT: F  105 MET cc_start: 0.8097 (tpt) cc_final: 0.7834 (ttp)
REVERT: F  235 ASP cc_start: 0.6856 (m-30) cc_final: 0.6421 (t0)
  outliers start: 20
  outliers final: 16
  residues processed: 200
  average time/residue: 0.1102
  time to fit residues: 29.5849
Evaluate side-chains
  204 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 187
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue  158 THR
Chi-restraints excluded: chain C residue  208 ARG
Chi-restraints excluded: chain D residue   51 THR
Chi-restraints excluded: chain E residue   49 LYS
Chi-restraints excluded: chain E residue  103 THR
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain F residue   49 LYS
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue  103 THR
Chi-restraints excluded: chain F residue  155 MET
Chi-restraints excluded: chain F residue  169 MET
Chi-restraints excluded: chain F residue  179 MET
Chi-restraints excluded: chain G residue   35 ILE
Chi-restraints excluded: chain G residue  155 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 37 optimal weight:   10.0000
   chunk 92 optimal weight:    1.9990
   chunk 101 optimal weight:   10.0000
   chunk 80 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 77 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9980
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.3965 r_free = 0.3965 target = 0.177765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.129793 restraints weight = 16130.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 2.11
r_work: 0.3091 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3057
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3057 r_free = 0.3057    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3057 r_free = 0.3057    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3057
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9035  Z= 0.132
  Angle     :  0.510   7.520  12169  Z= 0.263
  Chirality :  0.037   0.206   1447
  Planarity :  0.004   0.042   1544
  Dihedral  :  3.509  13.721   1223
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 25.19 %
    Favored  : 72.69 %
  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:  3.57 (0.24), residues: 1149
  helix:  2.77 (0.16), residues: 995
  sheet:  None (None), residues: 0
  loop : -0.56 (0.49), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 216 
 TYR   0.011   0.001   TYR E 237 
 PHE   0.014   0.001   PHE E 143 
 TRP   0.005   0.001   TRP A  18 
 HIS   0.007   0.001   HIS E 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 9035)
  covalent geometry    : angle       0.51047 (12169)
  hydrogen bonds       : bond        0.03753 (  808)
  hydrogen bonds       : angle       3.53125 ( 2399)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 188
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8040 (mp)
REVERT: C  148 ASP cc_start: 0.7834 (m-30) cc_final: 0.7603 (m-30)
REVERT: C  179 MET cc_start: 0.7916 (ptm) cc_final: 0.7650 (ttt)
REVERT: C  219 MET cc_start: 0.6644 (ttp) cc_final: 0.6245 (ttt)
REVERT: D  207 ARG cc_start: 0.8948 (tpt-90) cc_final: 0.8701 (tpp80)
REVERT: D  208 ARG cc_start: 0.8302 (ttp80) cc_final: 0.7941 (ttp-170)
REVERT: E   72 GLU cc_start: 0.7450 (pm20) cc_final: 0.6774 (tt0)
REVERT: E   74 GLU cc_start: 0.7882 (mp0) cc_final: 0.7547 (mp0)
REVERT: E  128 ASP cc_start: 0.7879 (t0) cc_final: 0.7014 (t0)
REVERT: F   20 MET cc_start: 0.2720 (ptm) cc_final: 0.2297 (tmm)
REVERT: F  105 MET cc_start: 0.8284 (tpt) cc_final: 0.7796 (ttp)
REVERT: F  235 ASP cc_start: 0.6829 (m-30) cc_final: 0.6500 (t0)
REVERT: G  105 MET cc_start: 0.7036 (tmm) cc_final: 0.6764 (tmm)
  outliers start: 20
  outliers final: 15
  residues processed: 197
  average time/residue: 0.1081
  time to fit residues: 28.4638
Evaluate side-chains
  199 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 183
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue  158 THR
Chi-restraints excluded: chain C residue  208 ARG
Chi-restraints excluded: chain E residue   49 LYS
Chi-restraints excluded: chain E residue   67 MET
Chi-restraints excluded: chain E residue  103 THR
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain F residue   49 LYS
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue  103 THR
Chi-restraints excluded: chain F residue  169 MET
Chi-restraints excluded: chain F residue  179 MET
Chi-restraints excluded: chain G residue   35 ILE
Chi-restraints excluded: chain G residue  155 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 64 optimal weight:    0.6980
   chunk 65 optimal weight:    0.5980
   chunk 79 optimal weight:    0.0170
   chunk 109 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 82 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.6218

-------------------------------------------------------------------------------
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 = 0.3997 r_free = 0.3997 target = 0.180485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 99)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.124309 restraints weight = 17416.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 2.17
r_work: 0.3087 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3055
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3055 r_free = 0.3055    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3055 r_free = 0.3055    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3055
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   9035  Z= 0.113
  Angle     :  0.496   8.021  12169  Z= 0.255
  Chirality :  0.036   0.201   1447
  Planarity :  0.004   0.042   1544
  Dihedral  :  3.492  14.435   1223
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 26.04 %
    Favored  : 72.58 %
  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:  3.77 (0.25), residues: 1149
  helix:  2.90 (0.16), residues: 995
  sheet:  None (None), residues: 0
  loop : -0.53 (0.50), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 216 
 TYR   0.011   0.001   TYR E 237 
 PHE   0.013   0.001   PHE E 143 
 TRP   0.008   0.001   TRP A  18 
 HIS   0.007   0.001   HIS E 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 9035)
  covalent geometry    : angle       0.49625 (12169)
  hydrogen bonds       : bond        0.03520 (  808)
  hydrogen bonds       : angle       3.48442 ( 2399)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 190
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  179 MET cc_start: 0.7881 (ptm) cc_final: 0.7656 (ttt)
REVERT: D   28 MET cc_start: 0.7255 (ttp) cc_final: 0.6792 (ttm)
REVERT: D  207 ARG cc_start: 0.8962 (tpt-90) cc_final: 0.8728 (tpp80)
REVERT: D  208 ARG cc_start: 0.8279 (ttp80) cc_final: 0.7952 (ttp-170)
REVERT: E   72 GLU cc_start: 0.7094 (pm20) cc_final: 0.6826 (tt0)
REVERT: E   74 GLU cc_start: 0.7969 (mp0) cc_final: 0.7331 (mp0)
REVERT: E  128 ASP cc_start: 0.7829 (t0) cc_final: 0.7008 (t0)
REVERT: F   20 MET cc_start: 0.2671 (ptm) cc_final: 0.2243 (tmm)
REVERT: F  105 MET cc_start: 0.8182 (tpt) cc_final: 0.7835 (ttp)
REVERT: F  235 ASP cc_start: 0.7118 (m-30) cc_final: 0.6677 (t0)
REVERT: G  105 MET cc_start: 0.6928 (tmm) cc_final: 0.6626 (tmm)
  outliers start: 13
  outliers final: 10
  residues processed: 196
  average time/residue: 0.1147
  time to fit residues: 30.0744
Evaluate side-chains
  193 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 183
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue  208 ARG
Chi-restraints excluded: chain E residue   49 LYS
Chi-restraints excluded: chain E residue  103 THR
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain F residue   49 LYS
Chi-restraints excluded: chain F residue  169 MET
Chi-restraints excluded: chain F residue  179 MET
Chi-restraints excluded: chain G residue  155 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 54 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 95 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 15 optimal weight:    6.9990
   overall best weight:    0.9380

-------------------------------------------------------------------------------
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 = 0.4001 r_free = 0.4001 target = 0.180855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.140535 restraints weight = 11527.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 3.29
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3504
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3504 r_free = 0.3504    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3504 r_free = 0.3504    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3504
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9035  Z= 0.122
  Angle     :  0.520   8.397  12169  Z= 0.265
  Chirality :  0.037   0.208   1447
  Planarity :  0.004   0.042   1544
  Dihedral  :  3.471  13.893   1223
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 25.82 %
    Favored  : 72.58 %
  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:  3.75 (0.25), residues: 1149
  helix:  2.88 (0.16), residues: 996
  sheet:  None (None), residues: 0
  loop : -0.48 (0.50), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 216 
 TYR   0.007   0.001   TYR E 237 
 PHE   0.020   0.001   PHE C  56 
 TRP   0.006   0.001   TRP A  18 
 HIS   0.007   0.001   HIS E 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 9035)
  covalent geometry    : angle       0.52004 (12169)
  hydrogen bonds       : bond        0.03603 (  808)
  hydrogen bonds       : angle       3.48332 ( 2399)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2322.95 seconds
wall clock time: 40 minutes 30.13 seconds (2430.13 seconds total)