Starting phenix.real_space_refine
on Wed Feb 12 06:51:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gse_34233/02_2025/8gse_34233.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gse_34233/02_2025/8gse_34233.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gse_34233/02_2025/8gse_34233.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gse_34233/02_2025/8gse_34233.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gse_34233/02_2025/8gse_34233.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gse_34233/02_2025/8gse_34233.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.008
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      47      5.16       5
     C    4751      2.51       5
     N    1252      2.21       5
     O    1424      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7474
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "1"
      Number of atoms: 1900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1900
          Classifications: {'peptide': 237}
          Link IDs: {'PTRANS': 17, 'TRANS': 219}
    Chain: "2"
      Number of atoms: 1964
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 250, 1964
          Classifications: {'peptide': 250}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 238}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "3"
      Number of atoms: 1816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1816
          Classifications: {'peptide': 234}
          Link IDs: {'PTRANS': 18, 'TRANS': 215}
    Chain: "H"
      Number of atoms: 907
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 907
          Classifications: {'peptide': 117}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 111}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "L"
      Number of atoms: 887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 887
          Classifications: {'peptide': 114}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
  Time building chain proxies: 5.43, per 1000 atoms: 0.73
  Number of scatterers: 7474
  At special positions: 0
  Unit cell: (110.7, 86.4, 132.3, 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      47     16.00
     O    1424      8.00
     N    1252      7.00
     C    4751      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  23 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.61
  Conformation dependent library (CDL) restraints added in 995.2 milliseconds
  

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1776

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 15 sheets defined
      10.9% alpha, 32.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain '1' and resid 59 through 62
    Processing helix  chain '1' and resid 63 through 69
    Processing helix  chain '1' and resid 100 through 109
    Processing helix  chain '1' and resid 159 through 164
    Processing helix  chain '2' and resid 152 through 156
    Processing helix  chain '2' and resid 158 through 168
      removed outlier: 3.767A  pdb=" N   GLY 2 162 " --> pdb=" O   MET 2 158 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 211 through 216
      removed outlier: 3.937A  pdb=" N   LEU 2 215 " --> pdb=" O   VAL 2 211 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   SER 2 216 " --> pdb=" O   ALA 2 212 " (cutoff:3.500A)
      No H-bonds generated for 'chain '2' and resid 211 through 216'
    Processing helix  chain '2' and resid 238 through 242
    Processing helix  chain '2' and resid 247 through 254
      removed outlier: 3.816A  pdb=" N   LEU 2 251 " --> pdb=" O   VAL 2 248 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   THR 2 252 " --> pdb=" O   GLY 2 249 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE 2 253 " --> pdb=" O   ASN 2 250 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 7 through 11
      removed outlier: 3.572A  pdb=" N   ASN 3  11 " --> pdb=" O   PRO 3   8 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 43 through 48
      removed outlier: 3.574A  pdb=" N   ALA 3  47 " --> pdb=" O   LEU 3  43 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLU 3  48 " --> pdb=" O   MET 3  44 " (cutoff:3.500A)
      No H-bonds generated for 'chain '3' and resid 43 through 48'
    Processing helix  chain '3' and resid 64 through 69
      removed outlier: 3.646A  pdb=" N   ALA 3  67 " --> pdb=" O   SER 3  64 " (cutoff:3.500A)
    Processing helix  chain '3' and resid 98 through 105
    Processing helix  chain '3' and resid 144 through 150
    Processing helix  chain 'H' and resid 61 through 65
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.829A  pdb=" N   ASP H  90 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   SER H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 87 through 91'
    Processing sheet with id=AA1, first strand: chain '1' and resid 72 through 79
      removed outlier: 6.690A  pdb=" N   VAL 1 238 " --> pdb=" O   VAL 1  74 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   ILE 1  76 " --> pdb=" O   LEU 1 236 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   LEU 1 236 " --> pdb=" O   ILE 1  76 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   THR 1  78 " --> pdb=" O   SER 1 234 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   SER 1 234 " --> pdb=" O   THR 1  78 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LYS 1 243 " --> pdb=" O   ASP 1 116 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   VAL 1 245 " --> pdb=" O   ARG 1 114 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   ARG 1 114 " --> pdb=" O   VAL 1 245 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   ALA 1 247 " --> pdb=" O   TYR 1 112 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   TYR 1 112 " --> pdb=" O   ALA 1 247 " (cutoff:3.500A)
      removed outlier: 7.388A  pdb=" N   VAL 1 249 " --> pdb=" O   PHE 1 110 " (cutoff:3.500A)
      removed outlier: 5.221A  pdb=" N   PHE 1 110 " --> pdb=" O   VAL 1 249 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ALA 1 179 " --> pdb=" O   PHE 1 121 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain '1' and resid 72 through 79
      removed outlier: 6.690A  pdb=" N   VAL 1 238 " --> pdb=" O   VAL 1  74 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   ILE 1  76 " --> pdb=" O   LEU 1 236 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   LEU 1 236 " --> pdb=" O   ILE 1  76 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   THR 1  78 " --> pdb=" O   SER 1 234 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   SER 1 234 " --> pdb=" O   THR 1  78 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LYS 1 243 " --> pdb=" O   ASP 1 116 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   VAL 1 245 " --> pdb=" O   ARG 1 114 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   ARG 1 114 " --> pdb=" O   VAL 1 245 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   ALA 1 247 " --> pdb=" O   TYR 1 112 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   TYR 1 112 " --> pdb=" O   ALA 1 247 " (cutoff:3.500A)
      removed outlier: 7.388A  pdb=" N   VAL 1 249 " --> pdb=" O   PHE 1 110 " (cutoff:3.500A)
      removed outlier: 5.221A  pdb=" N   PHE 1 110 " --> pdb=" O   VAL 1 249 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain '1' and resid 90 through 94
    Processing sheet with id=AA4, first strand: chain '2' and resid 83 through 84
    Processing sheet with id=AA5, first strand: chain '2' and resid 133 through 140
      removed outlier: 5.298A  pdb=" N   THR 2 134 " --> pdb=" O   VAL 2 314 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   VAL 2 314 " --> pdb=" O   THR 2 134 " (cutoff:3.500A)
      removed outlier: 5.360A  pdb=" N   ASP 2 136 " --> pdb=" O   VAL 2 312 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   VAL 2 312 " --> pdb=" O   ASP 2 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain '2' and resid 133 through 140
      removed outlier: 5.298A  pdb=" N   THR 2 134 " --> pdb=" O   VAL 2 314 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   VAL 2 314 " --> pdb=" O   THR 2 134 " (cutoff:3.500A)
      removed outlier: 5.360A  pdb=" N   ASP 2 136 " --> pdb=" O   VAL 2 312 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   VAL 2 312 " --> pdb=" O   ASP 2 136 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   ARG 2 172 " --> pdb=" O   ALA 2 319 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   ALA 2 319 " --> pdb=" O   ARG 2 172 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain '2' and resid 222 through 223
      removed outlier: 3.685A  pdb=" N   LYS 2 222 " --> pdb=" O   TRP 2 148 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   CYS 2 190 " --> pdb=" O   PHE 2 295 " (cutoff:3.500A)
      removed outlier: 5.911A  pdb=" N   LYS 2 297 " --> pdb=" O   GLN 2 188 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   GLN 2 188 " --> pdb=" O   LYS 2 297 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain '3' and resid 51 through 52
      removed outlier: 3.600A  pdb=" N   SER 3  51 " --> pdb=" O   ALA 3 214 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   VAL 3  72 " --> pdb=" O   CYS 3 208 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain '3' and resid 51 through 52
      removed outlier: 3.600A  pdb=" N   SER 3  51 " --> pdb=" O   ALA 3 214 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain '3' and resid 81 through 86
      removed outlier: 7.149A  pdb=" N   GLN 3  81 " --> pdb=" O   TYR 3 194 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   TYR 3 194 " --> pdb=" O   GLN 3  81 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   PHE 3  83 " --> pdb=" O   CYS 3 192 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   TYR 3 189 " --> pdb=" O   SER 3 135 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   THR 3 152 " --> pdb=" O   TYR 3 134 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain '3' and resid 177 through 178
      removed outlier: 3.507A  pdb=" N   ARG 3 177 " --> pdb=" O   TRP 3 110 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   TYR 3 107 " --> pdb=" O   LEU 3 225 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   LEU 3 225 " --> pdb=" O   TYR 3 107 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 57 through 58
      removed outlier: 3.845A  pdb=" N   ASP H  57 " --> pdb=" O   TYR H  52 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   TYR H  52 " --> pdb=" O   ASP H  57 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   TRP H  47 " --> pdb=" O   LYS H  38 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   LYS H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   TRP H  36 " --> pdb=" O   GLY H  49 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 68 through 71
      removed outlier: 3.542A  pdb=" N   THR H  69 " --> pdb=" O   GLN H  82 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   THR H  71 " --> pdb=" O   TYR H  80 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 5
    Processing sheet with id=AB6, first strand: chain 'L' and resid 59 through 60
      removed outlier: 6.683A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
      removed outlier: 5.173A  pdb=" N   TYR L  55 " --> pdb=" O   LEU L  39 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   LEU L  39 " --> pdb=" O   TYR L  55 " (cutoff:3.500A)

    196 hydrogen bonds defined for protein.
    486 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: 1.97

  Time building geometry restraints manager: 1.92 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2395
        1.34 -     1.46: 1887
        1.46 -     1.58: 3326
        1.58 -     1.70: 0
        1.70 -     1.81: 73
  Bond restraints: 7681
  Sorted by residual:
  bond pdb=" CB  PHE 3 220 "
       pdb=" CG  PHE 3 220 "
    ideal  model  delta    sigma   weight residual
    1.502  1.473  0.029 2.30e-02 1.89e+03 1.61e+00
  bond pdb=" CA  ILE 3 168 "
       pdb=" CB  ILE 3 168 "
    ideal  model  delta    sigma   weight residual
    1.533  1.521  0.013 1.05e-02 9.07e+03 1.45e+00
  bond pdb=" C   PHE 2 254 "
       pdb=" N   PRO 2 255 "
    ideal  model  delta    sigma   weight residual
    1.332  1.345 -0.013 1.12e-02 7.97e+03 1.37e+00
  bond pdb=" N   ILE 2 293 "
       pdb=" CA  ILE 2 293 "
    ideal  model  delta    sigma   weight residual
    1.454  1.463 -0.009 7.70e-03 1.69e+04 1.34e+00
  bond pdb=" C   THR 3 196 "
       pdb=" N   GLY 3 197 "
    ideal  model  delta    sigma   weight residual
    1.334  1.322  0.012 1.12e-02 7.97e+03 1.24e+00
  ... (remaining 7676 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 10273
        2.07 -     4.14: 189
        4.14 -     6.21: 8
        6.21 -     8.28: 0
        8.28 -    10.35: 1
  Bond angle restraints: 10471
  Sorted by residual:
  angle pdb=" N   VAL 2 102 "
        pdb=" CA  VAL 2 102 "
        pdb=" C   VAL 2 102 "
      ideal   model   delta    sigma   weight residual
     111.91  108.18    3.73 8.90e-01 1.26e+00 1.75e+01
  angle pdb=" C   TYR H  32 "
        pdb=" N   GLY H  33 "
        pdb=" CA  GLY H  33 "
      ideal   model   delta    sigma   weight residual
     121.61  118.58    3.03 7.70e-01 1.69e+00 1.55e+01
  angle pdb=" N   VAL 2 248 "
        pdb=" CA  VAL 2 248 "
        pdb=" C   VAL 2 248 "
      ideal   model   delta    sigma   weight residual
     113.00  108.89    4.11 1.30e+00 5.92e-01 9.99e+00
  angle pdb=" N   ASP 1 136 "
        pdb=" CA  ASP 1 136 "
        pdb=" C   ASP 1 136 "
      ideal   model   delta    sigma   weight residual
     110.06  114.41   -4.35 1.43e+00 4.89e-01 9.25e+00
  angle pdb=" N   PHE 3 220 "
        pdb=" CA  PHE 3 220 "
        pdb=" C   PHE 3 220 "
      ideal   model   delta    sigma   weight residual
     110.35  114.20   -3.85 1.36e+00 5.41e-01 8.01e+00
  ... (remaining 10466 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.51: 4083
       17.51 -    35.01: 351
       35.01 -    52.52: 62
       52.52 -    70.03: 10
       70.03 -    87.53: 10
  Dihedral angle restraints: 4516
    sinusoidal: 1742
      harmonic: 2774
  Sorted by residual:
  dihedral pdb=" CA  PHE 3 220 "
           pdb=" C   PHE 3 220 "
           pdb=" N   SER 3 221 "
           pdb=" CA  SER 3 221 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.86   25.14     0      5.00e+00 4.00e-02 2.53e+01
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  94 "
           pdb=" CB  CYS L  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   57.81   35.19     1      1.00e+01 1.00e-02 1.75e+01
  dihedral pdb=" CA  GLU 3 102 "
           pdb=" C   GLU 3 102 "
           pdb=" N   ILE 3 103 "
           pdb=" CA  ILE 3 103 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.36   16.64     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 4513 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 939
       0.058 -    0.117: 181
       0.117 -    0.175: 17
       0.175 -    0.233: 0
       0.233 -    0.292: 2
  Chirality restraints: 1139
  Sorted by residual:
  chirality pdb=" CB  ILE 3 231 "
            pdb=" CA  ILE 3 231 "
            pdb=" CG1 ILE 3 231 "
            pdb=" CG2 ILE 3 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.29 2.00e-01 2.50e+01 2.13e+00
  chirality pdb=" CB  ILE 1 186 "
            pdb=" CA  ILE 1 186 "
            pdb=" CG1 ILE 1 186 "
            pdb=" CG2 ILE 1 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.29 2.00e-01 2.50e+01 2.06e+00
  chirality pdb=" CA  ASN 1 211 "
            pdb=" N   ASN 1 211 "
            pdb=" C   ASN 1 211 "
            pdb=" CB  ASN 1 211 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.15e-01
  ... (remaining 1136 not shown)

  Planarity restraints: 1351
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE 3 220 "    0.029 2.00e-02 2.50e+03   2.34e-02 9.60e+00
        pdb=" CG  PHE 3 220 "   -0.053 2.00e-02 2.50e+03
        pdb=" CD1 PHE 3 220 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE 3 220 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE 3 220 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE 3 220 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE 3 220 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR 3 228 "    0.034 5.00e-02 4.00e+02   5.18e-02 4.29e+00
        pdb=" N   PRO 3 229 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO 3 229 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO 3 229 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  36 "   -0.012 2.00e-02 2.50e+03   1.18e-02 3.47e+00
        pdb=" CG  TRP H  36 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  36 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  36 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  36 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  36 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  36 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  36 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  36 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  36 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1348 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1546
        2.78 -     3.31: 6334
        3.31 -     3.84: 11250
        3.84 -     4.37: 12980
        4.37 -     4.90: 23811
  Nonbonded interactions: 55921
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP 2 280 "
            pdb=" N   ASN 2 281 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" OG1 THR 2 252 "
            pdb=" O   ASP 3  50 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OE2 GLU 3  66 "
            pdb=" NH1 ARG 3  69 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" OD2 ASP 3 182 "
            pdb=" OH  TYR 3 184 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" NH2 ARG 2 262 "
            pdb=" O   VAL 3 158 "
     model   vdw
     2.300 3.120
  ... (remaining 55916 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.590
  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:          0.260
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     20.230
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
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      :  0.005   0.040   7681  Z= 0.311
  Angle     :  0.676  10.354  10471  Z= 0.396
  Chirality :  0.046   0.292   1139
  Planarity :  0.005   0.052   1351
  Dihedral  : 13.931  87.533   2734
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.26), residues: 942
  helix: -1.62 (0.70), residues: 48
  sheet: -0.04 (0.34), residues: 257
  loop : -1.92 (0.22), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP H  36 
 HIS   0.007   0.001   HIS 1 223 
 PHE   0.053   0.002   PHE 3 220 
 TYR   0.025   0.002   TYR 3 107 
 ARG   0.007   0.001   ARG 2 208 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.871 
Fit side-chains
REVERT: 2  148 TRP cc_start: 0.7953 (p-90) cc_final: 0.7414 (p-90)
REVERT: 2  303 GLN cc_start: 0.5311 (tt0) cc_final: 0.4833 (pp30)
REVERT: 3   34 MET cc_start: 0.8738 (ptm) cc_final: 0.8301 (ptm)
REVERT: 3   35 LYS cc_start: 0.8894 (mmtm) cc_final: 0.8553 (tttp)
REVERT: H   91 SER cc_start: 0.4209 (m) cc_final: 0.3478 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.2235
  time to fit residues: 31.1587
Evaluate side-chains
  89 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 70 optimal weight:    8.9990
   chunk 39 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 37 optimal weight:    7.9990
   chunk 72 optimal weight:   20.0000
   chunk 28 optimal weight:    5.9990
   chunk 44 optimal weight:    0.4980
   chunk 54 optimal weight:    0.8980
   chunk 84 optimal weight:   30.0000
   overall best weight:    2.2584

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

Flipped N/Q/H residues before XYZ refinement:
3 109 HIS
L   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.164140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.126936 restraints weight = 9566.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.124123 restraints weight = 24660.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.119785 restraints weight = 24339.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.0825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7681  Z= 0.211
  Angle     :  0.524   9.616  10471  Z= 0.275
  Chirality :  0.043   0.209   1139
  Planarity :  0.005   0.047   1351
  Dihedral  :  4.522  16.801   1034
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  5.33 %
    Favored  : 93.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.26), residues: 942
  helix: -1.67 (0.70), residues: 50
  sheet: -0.01 (0.34), residues: 266
  loop : -1.73 (0.23), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  36 
 HIS   0.005   0.001   HIS 1 292 
 PHE   0.028   0.001   PHE 3 220 
 TYR   0.013   0.001   TYR 3 107 
 ARG   0.004   0.000   ARG 2 262 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 1.293 
Fit side-chains
REVERT: 2  148 TRP cc_start: 0.8110 (p-90) cc_final: 0.7678 (p-90)
REVERT: 2  303 GLN cc_start: 0.5158 (tt0) cc_final: 0.4928 (pp30)
REVERT: 3  220 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.6685 (m-80)
  outliers start: 6
  outliers final: 4
  residues processed: 100
  average time/residue: 0.2248
  time to fit residues: 30.0670
Evaluate side-chains
  96 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  278 ILE
Chi-restraints excluded: chain 2 residue   87 LEU
Chi-restraints excluded: chain 3 residue  103 ILE
Chi-restraints excluded: chain 3 residue  220 PHE
Chi-restraints excluded: chain L residue   82 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 1 optimal weight:    8.9990
   chunk 4 optimal weight:    8.9990
   chunk 89 optimal weight:    0.9990
   chunk 87 optimal weight:    0.4980
   chunk 52 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 78 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 90 optimal weight:    8.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
3 180 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.166969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.132177 restraints weight = 9486.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.130099 restraints weight = 21134.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.125703 restraints weight = 13815.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.1285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7681  Z= 0.131
  Angle     :  0.459   8.392  10471  Z= 0.239
  Chirality :  0.041   0.162   1139
  Planarity :  0.004   0.044   1351
  Dihedral  :  4.024  13.788   1034
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  8.97 %
    Favored  : 89.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.27), residues: 942
  helix: -1.52 (0.69), residues: 49
  sheet:  0.23 (0.34), residues: 269
  loop : -1.55 (0.24), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  36 
 HIS   0.004   0.001   HIS 1 223 
 PHE   0.021   0.001   PHE 3 220 
 TYR   0.011   0.001   TYR 3 107 
 ARG   0.005   0.000   ARG 1  94 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.801 
Fit side-chains
REVERT: 2  303 GLN cc_start: 0.5571 (tt0) cc_final: 0.4626 (pp30)
REVERT: 3   33 GLU cc_start: 0.8250 (pm20) cc_final: 0.7974 (pm20)
REVERT: 3   34 MET cc_start: 0.8516 (ptm) cc_final: 0.8294 (ptm)
REVERT: 3  220 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.6431 (m-80)
REVERT: H   35 GLN cc_start: 0.3906 (OUTLIER) cc_final: 0.0477 (tm-30)
  outliers start: 9
  outliers final: 4
  residues processed: 103
  average time/residue: 0.2117
  time to fit residues: 29.1652
Evaluate side-chains
  99 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  278 ILE
Chi-restraints excluded: chain 2 residue   97 CYS
Chi-restraints excluded: chain 2 residue  301 THR
Chi-restraints excluded: chain 3 residue  103 ILE
Chi-restraints excluded: chain 3 residue  220 PHE
Chi-restraints excluded: chain H residue   35 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 18 optimal weight:    3.9990
   chunk 49 optimal weight:    8.9990
   chunk 20 optimal weight:    0.3980
   chunk 21 optimal weight:    4.9990
   chunk 32 optimal weight:   10.0000
   chunk 77 optimal weight:    0.1980
   chunk 4 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   overall best weight:    1.5184

-------------------------------------------------------------------------------
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 = 0.3785 r_free = 0.3785 target = 0.166661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.130623 restraints weight = 9524.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.129484 restraints weight = 23229.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.123300 restraints weight = 23853.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.1439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7681  Z= 0.164
  Angle     :  0.482   7.327  10471  Z= 0.250
  Chirality :  0.042   0.163   1139
  Planarity :  0.004   0.040   1351
  Dihedral  :  3.953  13.308   1034
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 10.67 %
    Favored  : 87.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.27), residues: 942
  helix: -1.49 (0.69), residues: 49
  sheet:  0.35 (0.34), residues: 272
  loop : -1.53 (0.23), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP 2 148 
 HIS   0.004   0.001   HIS 1 223 
 PHE   0.024   0.001   PHE 3 220 
 TYR   0.010   0.001   TYR 2 240 
 ARG   0.004   0.000   ARG 1  94 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.768 
Fit side-chains
REVERT: 2  133 TYR cc_start: 0.9148 (m-80) cc_final: 0.8916 (m-80)
REVERT: 2  201 MET cc_start: 0.8885 (mmt) cc_final: 0.8513 (mmt)
REVERT: 2  215 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8309 (mp)
REVERT: 2  303 GLN cc_start: 0.5642 (tt0) cc_final: 0.5034 (pp30)
REVERT: 3   33 GLU cc_start: 0.8414 (pm20) cc_final: 0.8127 (pm20)
REVERT: 3   34 MET cc_start: 0.8608 (ptm) cc_final: 0.8043 (ptm)
REVERT: 3  220 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.6439 (m-80)
REVERT: H   35 GLN cc_start: 0.2211 (OUTLIER) cc_final: -0.0830 (tm-30)
  outliers start: 13
  outliers final: 7
  residues processed: 104
  average time/residue: 0.2235
  time to fit residues: 30.8318
Evaluate side-chains
  105 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  263 ASN
Chi-restraints excluded: chain 1 residue  278 ILE
Chi-restraints excluded: chain 2 residue  215 LEU
Chi-restraints excluded: chain 2 residue  238 VAL
Chi-restraints excluded: chain 2 residue  244 MET
Chi-restraints excluded: chain 2 residue  301 THR
Chi-restraints excluded: chain 3 residue  103 ILE
Chi-restraints excluded: chain 3 residue  220 PHE
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain L residue   82 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 40 optimal weight:    6.9990
   chunk 55 optimal weight:    3.9990
   chunk 1 optimal weight:    8.9990
   chunk 50 optimal weight:    8.9990
   chunk 83 optimal weight:    7.9990
   chunk 81 optimal weight:   30.0000
   chunk 31 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 14 optimal weight:    7.9990
   chunk 7 optimal weight:   20.0000
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
1 201 HIS
** 3 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.158548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.121572 restraints weight = 9645.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.120120 restraints weight = 24940.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.120017 restraints weight = 22732.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.092   7681  Z= 0.565
  Angle     :  0.700   8.069  10471  Z= 0.375
  Chirality :  0.050   0.162   1139
  Planarity :  0.006   0.059   1351
  Dihedral  :  5.211  16.581   1034
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 11.15 %
    Favored  : 86.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.26), residues: 942
  helix: -2.04 (0.66), residues: 49
  sheet: -0.07 (0.35), residues: 261
  loop : -2.10 (0.22), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP 2 148 
 HIS   0.006   0.002   HIS 3  41 
 PHE   0.037   0.003   PHE 3 220 
 TYR   0.017   0.002   TYR 2 240 
 ARG   0.004   0.001   ARG 1 222 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.860 
Fit side-chains
REVERT: 1  181 MET cc_start: 0.8609 (ptp) cc_final: 0.8375 (ptp)
REVERT: 1  236 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8812 (tp)
REVERT: 2  148 TRP cc_start: 0.8113 (p-90) cc_final: 0.7487 (p-90)
REVERT: 2  201 MET cc_start: 0.8926 (mmt) cc_final: 0.8478 (mmt)
REVERT: 2  303 GLN cc_start: 0.5440 (tt0) cc_final: 0.4837 (pp30)
REVERT: 3  220 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.7865 (m-80)
REVERT: H   35 GLN cc_start: 0.4857 (OUTLIER) cc_final: 0.0074 (tt0)
REVERT: L  112 ILE cc_start: 0.2683 (OUTLIER) cc_final: 0.2284 (tt)
  outliers start: 21
  outliers final: 11
  residues processed: 111
  average time/residue: 0.2125
  time to fit residues: 31.5212
Evaluate side-chains
  106 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  236 LEU
Chi-restraints excluded: chain 1 residue  278 ILE
Chi-restraints excluded: chain 2 residue   87 LEU
Chi-restraints excluded: chain 2 residue   97 CYS
Chi-restraints excluded: chain 2 residue  227 THR
Chi-restraints excluded: chain 2 residue  238 VAL
Chi-restraints excluded: chain 2 residue  244 MET
Chi-restraints excluded: chain 2 residue  301 THR
Chi-restraints excluded: chain 2 residue  302 GLU
Chi-restraints excluded: chain 3 residue  220 PHE
Chi-restraints excluded: chain 3 residue  221 SER
Chi-restraints excluded: chain 3 residue  222 VAL
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain L residue   82 SER
Chi-restraints excluded: chain L residue  112 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 91 optimal weight:   20.0000
   chunk 41 optimal weight:    0.0870
   chunk 47 optimal weight:    9.9990
   chunk 60 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0980
   overall best weight:    1.2364

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

Flipped N/Q/H residues before XYZ refinement:
2 168 HIS
3 105 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.163653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.120787 restraints weight = 9510.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.119137 restraints weight = 20527.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.120265 restraints weight = 19702.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7681  Z= 0.153
  Angle     :  0.504   9.196  10471  Z= 0.263
  Chirality :  0.042   0.158   1139
  Planarity :  0.004   0.042   1351
  Dihedral  :  4.402  16.611   1034
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 13.33 %
    Favored  : 85.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.26), residues: 942
  helix: -1.71 (0.70), residues: 48
  sheet:  0.21 (0.34), residues: 278
  loop : -1.82 (0.22), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP 2 148 
 HIS   0.003   0.001   HIS 1 223 
 PHE   0.029   0.001   PHE 3 220 
 TYR   0.015   0.001   TYR 3 184 
 ARG   0.004   0.000   ARG H  98 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.820 
Fit side-chains
REVERT: 2  148 TRP cc_start: 0.7974 (p-90) cc_final: 0.7479 (p-90)
REVERT: 2  201 MET cc_start: 0.8878 (mmt) cc_final: 0.8527 (mmt)
REVERT: 2  303 GLN cc_start: 0.5468 (tt0) cc_final: 0.4874 (pp30)
REVERT: 3   33 GLU cc_start: 0.8240 (pm20) cc_final: 0.7980 (pm20)
REVERT: 3  184 TYR cc_start: 0.7842 (m-80) cc_final: 0.7550 (m-80)
REVERT: 3  220 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.7393 (m-80)
REVERT: H   35 GLN cc_start: 0.3941 (OUTLIER) cc_final: -0.0236 (tt0)
REVERT: H   81 MET cc_start: 0.2138 (ttp) cc_final: 0.1879 (ttp)
  outliers start: 12
  outliers final: 7
  residues processed: 105
  average time/residue: 0.2045
  time to fit residues: 28.9119
Evaluate side-chains
  101 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  278 ILE
Chi-restraints excluded: chain 2 residue   97 CYS
Chi-restraints excluded: chain 2 residue  238 VAL
Chi-restraints excluded: chain 2 residue  244 MET
Chi-restraints excluded: chain 2 residue  301 THR
Chi-restraints excluded: chain 3 residue  103 ILE
Chi-restraints excluded: chain 3 residue  220 PHE
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain L residue   82 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 83 optimal weight:    0.5980
   chunk 68 optimal weight:    3.9990
   chunk 29 optimal weight:    9.9990
   chunk 36 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 24 optimal weight:   20.0000
   chunk 23 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 87 optimal weight:    8.9990
   overall best weight:    3.5188

-------------------------------------------------------------------------------
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 = 0.3735 r_free = 0.3735 target = 0.161828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.118475 restraints weight = 9514.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.116508 restraints weight = 17885.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.117844 restraints weight = 17256.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   7681  Z= 0.300
  Angle     :  0.549   8.400  10471  Z= 0.289
  Chirality :  0.044   0.164   1139
  Planarity :  0.005   0.044   1351
  Dihedral  :  4.543  17.934   1034
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 13.94 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.84 (0.26), residues: 942
  helix: -1.85 (0.68), residues: 48
  sheet:  0.16 (0.34), residues: 266
  loop : -1.92 (0.22), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP 2 148 
 HIS   0.004   0.001   HIS 3  41 
 PHE   0.032   0.002   PHE 3 220 
 TYR   0.018   0.001   TYR 3 184 
 ARG   0.006   0.001   ARG 2 208 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.865 
Fit side-chains
REVERT: 2  148 TRP cc_start: 0.8030 (p-90) cc_final: 0.7526 (p-90)
REVERT: 2  201 MET cc_start: 0.8930 (mmt) cc_final: 0.8563 (mmt)
REVERT: 2  303 GLN cc_start: 0.5480 (tt0) cc_final: 0.4881 (pp30)
REVERT: 3   33 GLU cc_start: 0.8304 (pm20) cc_final: 0.8031 (pm20)
REVERT: 3  184 TYR cc_start: 0.7847 (m-80) cc_final: 0.7565 (m-80)
REVERT: 3  220 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.7775 (m-80)
REVERT: H   35 GLN cc_start: 0.4173 (OUTLIER) cc_final: -0.0189 (tt0)
REVERT: H   81 MET cc_start: 0.2555 (ttp) cc_final: 0.2224 (ttp)
  outliers start: 16
  outliers final: 10
  residues processed: 102
  average time/residue: 0.2155
  time to fit residues: 29.8483
Evaluate side-chains
  105 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  263 ASN
Chi-restraints excluded: chain 1 residue  278 ILE
Chi-restraints excluded: chain 2 residue   87 LEU
Chi-restraints excluded: chain 2 residue   97 CYS
Chi-restraints excluded: chain 2 residue  238 VAL
Chi-restraints excluded: chain 2 residue  301 THR
Chi-restraints excluded: chain 3 residue   53 VAL
Chi-restraints excluded: chain 3 residue  103 ILE
Chi-restraints excluded: chain 3 residue  220 PHE
Chi-restraints excluded: chain 3 residue  222 VAL
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain L residue   82 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 66 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 42 optimal weight:    0.4980
   chunk 58 optimal weight:    0.9990
   chunk 16 optimal weight:    6.9990
   chunk 82 optimal weight:    0.5980
   overall best weight:    0.8184

-------------------------------------------------------------------------------
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 = 0.3825 r_free = 0.3825 target = 0.169647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.124147 restraints weight = 9530.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.121550 restraints weight = 17715.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.123259 restraints weight = 16015.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7681  Z= 0.128
  Angle     :  0.478   8.484  10471  Z= 0.246
  Chirality :  0.042   0.160   1139
  Planarity :  0.004   0.043   1351
  Dihedral  :  4.025  15.940   1034
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 14.42 %
    Favored  : 84.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.26), residues: 942
  helix: -1.71 (0.69), residues: 48
  sheet:  0.38 (0.34), residues: 263
  loop : -1.73 (0.23), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP 2 148 
 HIS   0.003   0.000   HIS 1 223 
 PHE   0.026   0.001   PHE 3 220 
 TYR   0.014   0.001   TYR 3 184 
 ARG   0.007   0.000   ARG 2 208 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.846 
Fit side-chains
REVERT: 2  148 TRP cc_start: 0.7943 (p-90) cc_final: 0.7537 (p-90)
REVERT: 2  201 MET cc_start: 0.8917 (mmt) cc_final: 0.8509 (mmt)
REVERT: 2  280 ASP cc_start: 0.8284 (t0) cc_final: 0.8073 (t0)
REVERT: 2  303 GLN cc_start: 0.5663 (tt0) cc_final: 0.5037 (pp30)
REVERT: 3   33 GLU cc_start: 0.8236 (pm20) cc_final: 0.7962 (pm20)
REVERT: 3  184 TYR cc_start: 0.7346 (m-80) cc_final: 0.7100 (m-80)
REVERT: 3  220 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.7331 (m-80)
REVERT: H   35 GLN cc_start: 0.3322 (OUTLIER) cc_final: -0.0097 (tm-30)
REVERT: H   81 MET cc_start: 0.2360 (ttp) cc_final: 0.2103 (ttp)
  outliers start: 11
  outliers final: 7
  residues processed: 107
  average time/residue: 0.2019
  time to fit residues: 29.2361
Evaluate side-chains
  104 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  263 ASN
Chi-restraints excluded: chain 1 residue  278 ILE
Chi-restraints excluded: chain 2 residue   97 CYS
Chi-restraints excluded: chain 2 residue  238 VAL
Chi-restraints excluded: chain 2 residue  301 THR
Chi-restraints excluded: chain 3 residue  103 ILE
Chi-restraints excluded: chain 3 residue  220 PHE
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain L residue   82 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 18 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9980
   chunk 31 optimal weight:    6.9990
   chunk 39 optimal weight:    4.9990
   chunk 68 optimal weight:    0.7980
   chunk 81 optimal weight:    9.9990
   chunk 27 optimal weight:    0.6980
   chunk 84 optimal weight:   30.0000
   chunk 91 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.2982

-------------------------------------------------------------------------------
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 = 0.3780 r_free = 0.3780 target = 0.165698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.124337 restraints weight = 9537.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.122795 restraints weight = 18608.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.123504 restraints weight = 19366.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7681  Z= 0.151
  Angle     :  0.480   7.441  10471  Z= 0.248
  Chirality :  0.042   0.161   1139
  Planarity :  0.004   0.044   1351
  Dihedral  :  3.922  15.458   1034
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 15.76 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.26), residues: 942
  helix: -1.66 (0.69), residues: 48
  sheet:  0.46 (0.35), residues: 258
  loop : -1.70 (0.23), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP 2 148 
 HIS   0.003   0.001   HIS 1 223 
 PHE   0.026   0.001   PHE 3 220 
 TYR   0.014   0.001   TYR 3 184 
 ARG   0.006   0.000   ARG 2 208 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.903 
Fit side-chains
REVERT: 2  148 TRP cc_start: 0.8047 (p-90) cc_final: 0.7685 (p-90)
REVERT: 2  165 MET cc_start: 0.7832 (mtp) cc_final: 0.7554 (mtm)
REVERT: 2  303 GLN cc_start: 0.5518 (tt0) cc_final: 0.4933 (pp30)
REVERT: 3   33 GLU cc_start: 0.8198 (pm20) cc_final: 0.7963 (pm20)
REVERT: 3  184 TYR cc_start: 0.7497 (m-80) cc_final: 0.7192 (m-80)
REVERT: 3  220 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.6802 (m-80)
REVERT: H   81 MET cc_start: 0.2546 (ttp) cc_final: 0.2266 (ttt)
  outliers start: 8
  outliers final: 6
  residues processed: 100
  average time/residue: 0.2114
  time to fit residues: 28.4598
Evaluate side-chains
  103 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  263 ASN
Chi-restraints excluded: chain 1 residue  278 ILE
Chi-restraints excluded: chain 2 residue   97 CYS
Chi-restraints excluded: chain 2 residue  238 VAL
Chi-restraints excluded: chain 2 residue  301 THR
Chi-restraints excluded: chain 3 residue  220 PHE
Chi-restraints excluded: chain L residue   82 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 84 optimal weight:    0.0670
   chunk 89 optimal weight:    0.0570
   chunk 20 optimal weight:    0.7980
   chunk 75 optimal weight:   30.0000
   chunk 17 optimal weight:    2.9990
   chunk 80 optimal weight:   40.0000
   chunk 22 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 35 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.9840

-------------------------------------------------------------------------------
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 = 0.3830 r_free = 0.3830 target = 0.170041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.134126 restraints weight = 9630.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.132465 restraints weight = 21545.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.126910 restraints weight = 20747.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7681  Z= 0.134
  Angle     :  0.472   7.472  10471  Z= 0.242
  Chirality :  0.042   0.165   1139
  Planarity :  0.004   0.047   1351
  Dihedral  :  3.821  14.814   1034
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 15.76 %
    Favored  : 83.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.27), residues: 942
  helix: -1.98 (0.63), residues: 54
  sheet:  0.48 (0.35), residues: 251
  loop : -1.58 (0.23), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP 2 148 
 HIS   0.003   0.001   HIS 1 223 
 PHE   0.024   0.001   PHE 3 220 
 TYR   0.012   0.001   TYR 3 184 
 ARG   0.007   0.001   ARG 2 208 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.838 
Fit side-chains
REVERT: 2  148 TRP cc_start: 0.8054 (p-90) cc_final: 0.7668 (p-90)
REVERT: 2  165 MET cc_start: 0.7744 (mtp) cc_final: 0.7438 (mtm)
REVERT: 2  201 MET cc_start: 0.8980 (mmt) cc_final: 0.8399 (mmt)
REVERT: 2  303 GLN cc_start: 0.5484 (tt0) cc_final: 0.4902 (pp30)
REVERT: 3   33 GLU cc_start: 0.8209 (pm20) cc_final: 0.7986 (pm20)
REVERT: 3  184 TYR cc_start: 0.7543 (m-80) cc_final: 0.7271 (m-80)
REVERT: 3  220 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.6734 (m-80)
REVERT: H   35 GLN cc_start: 0.2565 (OUTLIER) cc_final: -0.0524 (tm-30)
  outliers start: 9
  outliers final: 6
  residues processed: 104
  average time/residue: 0.2108
  time to fit residues: 29.5477
Evaluate side-chains
  106 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  263 ASN
Chi-restraints excluded: chain 1 residue  278 ILE
Chi-restraints excluded: chain 2 residue   97 CYS
Chi-restraints excluded: chain 2 residue  238 VAL
Chi-restraints excluded: chain 2 residue  301 THR
Chi-restraints excluded: chain 3 residue  220 PHE
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain L residue   82 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 87 optimal weight:   20.0000
   chunk 35 optimal weight:    6.9990
   chunk 45 optimal weight:    6.9990
   chunk 37 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 30 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   chunk 2 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   overall best weight:    4.1388

-------------------------------------------------------------------------------
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 = 0.3727 r_free = 0.3727 target = 0.161148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.118290 restraints weight = 9572.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.116076 restraints weight = 15702.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.116255 restraints weight = 17054.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   7681  Z= 0.347
  Angle     :  0.569   7.438  10471  Z= 0.299
  Chirality :  0.045   0.153   1139
  Planarity :  0.005   0.049   1351
  Dihedral  :  4.441  17.980   1034
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 16.00 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.26), residues: 942
  helix: -1.90 (0.68), residues: 48
  sheet:  0.36 (0.34), residues: 263
  loop : -1.81 (0.22), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP 2 148 
 HIS   0.004   0.001   HIS 1 223 
 PHE   0.034   0.002   PHE 3 220 
 TYR   0.014   0.002   TYR 3 184 
 ARG   0.007   0.001   ARG 2 208 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2437.29 seconds
wall clock time: 44 minutes 58.44 seconds (2698.44 seconds total)