Starting phenix.real_space_refine
on Tue Feb 11 14:16:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pwc_20505/02_2025/6pwc_20505.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pwc_20505/02_2025/6pwc_20505.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6pwc_20505/02_2025/6pwc_20505.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pwc_20505/02_2025/6pwc_20505.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pwc_20505/02_2025/6pwc_20505.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pwc_20505/02_2025/6pwc_20505.cif"
  }
  resolution = 4.9
  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=  -0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      25      5.16       5
     C    3562      2.51       5
     N    1065      2.21       5
     O    1227      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5879
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 1824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 1824
          Classifications: {'peptide': 323}
          Incomplete info: {'truncation_to_alanine': 174}
          Link IDs: {'PTRANS': 10, 'TRANS': 312}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 779
          Unresolved non-hydrogen angles: 1003
          Unresolved non-hydrogen dihedrals: 677
          Unresolved non-hydrogen chiralities: 60
          Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 9, 'TYR:plan': 14, 'ASN:plan1': 13, 'TRP:plan': 4, 'ASP:plan': 8, 'PHE:plan': 17, 'GLU:plan': 6, 'ARG:plan': 15}
          Unresolved non-hydrogen planarities: 475
    Chain: "B"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 27
          Classifications: {'peptide': 5}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 3}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "A"
      Number of atoms: 1935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 350, 1935
          Classifications: {'peptide': 350}
          Incomplete info: {'truncation_to_alanine': 206}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 324}
          Unresolved non-hydrogen bonds: 863
          Unresolved non-hydrogen angles: 1078
          Unresolved non-hydrogen dihedrals: 721
          Unresolved non-hydrogen chiralities: 55
          Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 21, 'TYR:plan': 11, 'ASN:plan1': 14, 'HIS:plan': 8, 'PHE:plan': 12, 'GLU:plan': 24, 'ARG:plan': 20}
          Unresolved non-hydrogen planarities: 522
    Chain: "H"
      Number of atoms: 1072
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1072
          Classifications: {'peptide': 194}
          Incomplete info: {'truncation_to_alanine': 88}
          Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 184}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 445
          Unresolved non-hydrogen angles: 580
          Unresolved non-hydrogen dihedrals: 405
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 6, 'TYR:plan': 14, 'ASN:plan1': 7, 'TRP:plan': 5, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 307
    Chain: "L"
      Number of atoms: 1021
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 1021
          Classifications: {'peptide': 183}
          Incomplete info: {'truncation_to_alanine': 88}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 172}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 411
          Unresolved non-hydrogen angles: 522
          Unresolved non-hydrogen dihedrals: 360
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 1, 'TYR:plan': 10, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 7, 'GLU:plan': 6, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 278
  Time building chain proxies: 4.45, per 1000 atoms: 0.76
  Number of scatterers: 5879
  At special positions: 0
  Unit cell: (161.867, 106.193, 90.728, 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      25     16.00
     O    1227      8.00
     N    1065      7.00
     C    3562      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 141 " - pdb=" SG  CYS R 224 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 279 " - pdb=" SG  CYS H  59 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " 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: 1.54
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2000

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 17 sheets defined
      30.4% alpha, 29.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'R' and resid 59 through 91
    Processing helix  chain 'R' and resid 92 through 94
      No H-bonds generated for 'chain 'R' and resid 92 through 94'
    Processing helix  chain 'R' and resid 98 through 129
      Proline residue:  R 121  - end of helix
    Processing helix  chain 'R' and resid 137 through 172
    Processing helix  chain 'R' and resid 172 through 179
      removed outlier: 3.959A  pdb=" N   LYS R 177 " --> pdb=" O   PRO R 173 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 181 through 200
    Processing helix  chain 'R' and resid 201 through 205
    Processing helix  chain 'R' and resid 218 through 220
      No H-bonds generated for 'chain 'R' and resid 218 through 220'
    Processing helix  chain 'R' and resid 229 through 245
    Processing helix  chain 'R' and resid 245 through 269
      removed outlier: 3.694A  pdb=" N   VAL R 267 " --> pdb=" O   LEU R 263 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ARG R 268 " --> pdb=" O   THR R 264 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 294 through 329
      removed outlier: 3.848A  pdb=" N   VAL R 309 " --> pdb=" O   LEU R 305 " (cutoff:3.500A)
      Proline residue:  R 318  - end of helix
      removed outlier: 4.197A  pdb=" N   ARG R 323 " --> pdb=" O   TYR R 319 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE R 329 " --> pdb=" O   MET R 325 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 335 through 368
      removed outlier: 4.160A  pdb=" N   ASN R 360 " --> pdb=" O   SER R 356 " (cutoff:3.500A)
      Proline residue:  R 361  - end of helix
    Processing helix  chain 'R' and resid 368 through 383
    Processing helix  chain 'A' and resid 65 through 72
    Processing helix  chain 'A' and resid 98 through 109
    Processing helix  chain 'A' and resid 278 through 282
    Processing helix  chain 'H' and resid 31 through 33
      No H-bonds generated for 'chain 'H' and resid 31 through 33'
    Processing helix  chain 'H' and resid 90 through 94
    Processing helix  chain 'H' and resid 166 through 168
      No H-bonds generated for 'chain 'H' and resid 166 through 168'
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.775A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 122 through 127
    Processing helix  chain 'L' and resid 185 through 190
      removed outlier: 4.252A  pdb=" N   LYS L 189 " --> pdb=" O   ALA L 185 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 208 through 211
    Processing sheet with id=AA2, first strand: chain 'R' and resid 411 through 413
      removed outlier: 3.629A  pdb=" N   ASN R 411 " --> pdb=" O   LYS A  10 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   THR R 413 " --> pdb=" O   VAL A   8 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 29
      removed outlier: 5.898A  pdb=" N   PHE A  27 " --> pdb=" O   VAL A 171 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 77
      removed outlier: 4.036A  pdb=" N   PHE A  75 " --> pdb=" O   TYR A  63 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   VAL A  53 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 75 through 77
      removed outlier: 4.036A  pdb=" N   PHE A  75 " --> pdb=" O   TYR A  63 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 127 through 129
    Processing sheet with id=AA7, first strand: chain 'A' and resid 183 through 188
    Processing sheet with id=AA8, first strand: chain 'A' and resid 207 through 209
      removed outlier: 6.065A  pdb=" N   TYR A 208 " --> pdb=" O   MET A 352 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   TYR A 321 " --> pdb=" O   PHE A 349 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   SER A 330 " --> pdb=" O   VAL A 228 " (cutoff:3.500A)
      removed outlier: 5.154A  pdb=" N   VAL A 228 " --> pdb=" O   SER A 330 " (cutoff:3.500A)
      removed outlier: 5.858A  pdb=" N   GLN A 237 " --> pdb=" O   PRO A 252 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   ALA A 239 " --> pdb=" O   LYS A 250 " (cutoff:3.500A)
      removed outlier: 5.575A  pdb=" N   LYS A 250 " --> pdb=" O   ALA A 239 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AB1, first strand: chain 'H' and resid 13 through 15
      removed outlier: 5.888A  pdb=" N   ARG H  41 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   TRP H  50 " --> pdb=" O   ARG H  41 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 13 through 15
    Processing sheet with id=AB3, first strand: chain 'H' and resid 130 through 133
      removed outlier: 5.927A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   SER H 187 " --> pdb=" O   VAL H 179 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   VAL H 179 " --> pdb=" O   SER H 187 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 161 through 164
    Processing sheet with id=AB5, first strand: chain 'H' and resid 173 through 175
    Processing sheet with id=AB6, first strand: chain 'L' and resid 5 through 8
    Processing sheet with id=AB7, first strand: chain 'L' and resid 11 through 14
      removed outlier: 6.236A  pdb=" N   LEU L  12 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 5.608A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 115 through 119
      removed outlier: 6.105A  pdb=" N   TYR L 174 " --> pdb=" O   ASN L 139 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR L 179 " --> pdb=" O   GLN L 161 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   ASN L 159 " --> pdb=" O   THR L 181 " (cutoff:3.500A)

    429 hydrogen bonds defined for protein.
    1182 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: 2.18

  Time building geometry restraints manager: 1.75 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: 2088
        1.34 -     1.46: 1158
        1.46 -     1.58: 2664
        1.58 -     1.70: 0
        1.70 -     1.82: 25
  Bond restraints: 5935
  Sorted by residual:
  bond pdb=" C   LYS A 355 "
       pdb=" N   PRO A 356 "
    ideal  model  delta    sigma   weight residual
    1.341  1.376 -0.035 1.60e-02 3.91e+03 4.87e+00
  bond pdb=" C   MET R 120 "
       pdb=" N   PRO R 121 "
    ideal  model  delta    sigma   weight residual
    1.336  1.359 -0.023 1.20e-02 6.94e+03 3.52e+00
  bond pdb=" C   VAL R 201 "
       pdb=" N   PRO R 202 "
    ideal  model  delta    sigma   weight residual
    1.335  1.356 -0.022 1.19e-02 7.06e+03 3.35e+00
  bond pdb=" C   LEU R 317 "
       pdb=" N   PRO R 318 "
    ideal  model  delta    sigma   weight residual
    1.336  1.357 -0.022 1.25e-02 6.40e+03 2.98e+00
  bond pdb=" CA  VAL R 201 "
       pdb=" C   VAL R 201 "
    ideal  model  delta    sigma   weight residual
    1.523  1.537 -0.014 9.20e-03 1.18e+04 2.31e+00
  ... (remaining 5930 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 8005
        1.57 -     3.14: 236
        3.14 -     4.70: 21
        4.70 -     6.27: 12
        6.27 -     7.84: 6
  Bond angle restraints: 8280
  Sorted by residual:
  angle pdb=" C   ALA R 200 "
        pdb=" N   VAL R 201 "
        pdb=" CA  VAL R 201 "
      ideal   model   delta    sigma   weight residual
     120.33  125.09   -4.76 8.00e-01 1.56e+00 3.54e+01
  angle pdb=" CA  VAL R 201 "
        pdb=" C   VAL R 201 "
        pdb=" N   PRO R 202 "
      ideal   model   delta    sigma   weight residual
     120.83  122.82   -1.99 6.10e-01 2.69e+00 1.07e+01
  angle pdb=" C   SER L  51 "
        pdb=" N   ALA L  52 "
        pdb=" CA  ALA L  52 "
      ideal   model   delta    sigma   weight residual
     121.54  127.59   -6.05 1.91e+00 2.74e-01 1.00e+01
  angle pdb=" CA  LYS A  95 "
        pdb=" C   LYS A  95 "
        pdb=" N   PRO A  96 "
      ideal   model   delta    sigma   weight residual
     118.44  123.01   -4.57 1.59e+00 3.96e-01 8.25e+00
  angle pdb=" CA  GLY A 316 "
        pdb=" C   GLY A 316 "
        pdb=" N   ILE A 317 "
      ideal   model   delta    sigma   weight residual
     114.62  118.23   -3.61 1.26e+00 6.30e-01 8.20e+00
  ... (remaining 8275 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.22: 3517
       12.22 -    24.43: 24
       24.43 -    36.65: 2
       36.65 -    48.87: 3
       48.87 -    61.08: 2
  Dihedral angle restraints: 3548
    sinusoidal: 501
      harmonic: 3047
  Sorted by residual:
  dihedral pdb=" CB  CYS R 141 "
           pdb=" SG  CYS R 141 "
           pdb=" SG  CYS R 224 "
           pdb=" CB  CYS R 224 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  154.08  -61.08     1      1.00e+01 1.00e-02 4.96e+01
  dihedral pdb=" CB  CYS A 279 "
           pdb=" SG  CYS A 279 "
           pdb=" SG  CYS H  59 "
           pdb=" CB  CYS H  59 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -32.21  -53.79     1      1.00e+01 1.00e-02 3.93e+01
  dihedral pdb=" CA  TRP H 113 "
           pdb=" C   TRP H 113 "
           pdb=" N   GLY H 114 "
           pdb=" CA  GLY H 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.97   21.03     0      5.00e+00 4.00e-02 1.77e+01
  ... (remaining 3545 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 765
       0.036 -    0.072: 268
       0.072 -    0.109: 88
       0.109 -    0.145: 48
       0.145 -    0.181: 3
  Chirality restraints: 1172
  Sorted by residual:
  chirality pdb=" CA  THR R 115 "
            pdb=" N   THR R 115 "
            pdb=" C   THR R 115 "
            pdb=" CB  THR R 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.18 2.00e-01 2.50e+01 8.21e-01
  chirality pdb=" CA  MET R 120 "
            pdb=" N   MET R 120 "
            pdb=" C   MET R 120 "
            pdb=" CB  MET R 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.18 2.00e-01 2.50e+01 7.69e-01
  chirality pdb=" CA  LEU R 317 "
            pdb=" N   LEU R 317 "
            pdb=" C   LEU R 317 "
            pdb=" CB  LEU R 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.77e-01
  ... (remaining 1169 not shown)

  Planarity restraints: 1111
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R 225 "    0.030 5.00e-02 4.00e+02   4.60e-02 3.39e+00
        pdb=" N   PRO R 226 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO R 226 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO R 226 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 267 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.06e+00
        pdb=" C   VAL R 267 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   VAL R 267 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ARG R 268 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR R 144 "    0.018 2.00e-02 2.50e+03   1.23e-02 3.03e+00
        pdb=" CG  TYR R 144 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR R 144 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR R 144 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE1 TYR R 144 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR R 144 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  TYR R 144 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR R 144 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1108 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.86: 1987
        2.86 -     3.37: 5096
        3.37 -     3.88: 8881
        3.88 -     4.39: 7784
        4.39 -     4.90: 15405
  Nonbonded interactions: 39153
  Sorted by model distance:
  nonbonded pdb=" O   ASN R 240 "
            pdb=" OG  SER R 244 "
     model   vdw
     2.345 3.040
  nonbonded pdb=" O   TYR R 354 "
            pdb=" OG1 THR R 358 "
     model   vdw
     2.376 3.040
  nonbonded pdb=" O   HIS H 210 "
            pdb=" N   ASN H 214 "
     model   vdw
     2.380 3.120
  nonbonded pdb=" O   ALA A 301 "
            pdb=" OH  TYR A 321 "
     model   vdw
     2.393 3.040
  nonbonded pdb=" O   ALA A 263 "
            pdb=" OG  SER A 266 "
     model   vdw
     2.401 3.040
  ... (remaining 39148 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:             1.160
  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:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.950
  Find NCS groups from input model:        0.090
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6765
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   0.045   5935  Z= 0.223
  Angle     :  0.667   7.838   8280  Z= 0.392
  Chirality :  0.046   0.181   1172
  Planarity :  0.006   0.046   1111
  Dihedral  :  4.676  21.029   1536
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 2.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    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: -0.09 (0.24), residues: 1031
  helix:  0.54 (0.27), residues: 265
  sheet:  0.29 (0.28), residues: 327
  loop : -0.60 (0.27), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP R 193 
 HIS   0.007   0.004   HIS R 102 
 PHE   0.002   0.000   PHE R  74 
 TYR   0.029   0.002   TYR R 344 
 ARG   0.000   0.000   ARG R 372 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.619 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.0659
  time to fit residues: 4.3135
Evaluate side-chains
  19 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:   40.0000
   chunk 78 optimal weight:   40.0000
   chunk 43 optimal weight:    0.0000
   chunk 26 optimal weight:   30.0000
   chunk 53 optimal weight:   20.0000
   chunk 42 optimal weight:   10.0000
   chunk 81 optimal weight:    9.9990
   chunk 31 optimal weight:   50.0000
   chunk 49 optimal weight:   40.0000
   chunk 60 optimal weight:    1.9990
   chunk 94 optimal weight:   10.0000
   overall best weight:    6.3996

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

Flipped N/Q/H residues before XYZ refinement:
R 104 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.039996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.027699 restraints weight = 103705.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 15)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.027698 restraints weight = 105512.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.027698 restraints weight = 105530.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5556
moved from start:          0.3810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   5935  Z= 0.277
  Angle     :  0.653   6.582   8280  Z= 0.379
  Chirality :  0.042   0.167   1172
  Planarity :  0.005   0.066   1111
  Dihedral  :  5.146  22.129   1048
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  1.38 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    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:  0.57 (0.26), residues: 1031
  helix:  2.03 (0.30), residues: 273
  sheet: -0.45 (0.26), residues: 370
  loop :  0.23 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP R 193 
 HIS   0.006   0.003   HIS R 300 
 PHE   0.017   0.001   PHE A  80 
 TYR   0.019   0.001   TYR A 321 
 ARG   0.003   0.002   ARG R 372 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.696 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 21
  average time/residue: 0.0594
  time to fit residues: 3.2407
Evaluate side-chains
  17 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 16
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 26 optimal weight:    4.9990
   chunk 98 optimal weight:    6.9990
   chunk 61 optimal weight:    5.9990
   chunk 66 optimal weight:   20.0000
   chunk 29 optimal weight:   10.0000
   chunk 57 optimal weight:   30.0000
   chunk 60 optimal weight:    7.9990
   chunk 56 optimal weight:   30.0000
   chunk 68 optimal weight:    8.9990
   chunk 8 optimal weight:    9.9990
   overall best weight:    6.7990

-------------------------------------------------------------------------------
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 = 0.2916 r_free = 0.2916 target = 0.037705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2581 r_free = 0.2581 target = 0.025881 restraints weight = 105541.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2581 r_free = 0.2581 target = 0.025881 restraints weight = 106410.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2581 r_free = 0.2581 target = 0.025881 restraints weight = 106410.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5559
moved from start:          0.5304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5935  Z= 0.225
  Angle     :  0.557   7.686   8280  Z= 0.314
  Chirality :  0.041   0.161   1172
  Planarity :  0.005   0.057   1111
  Dihedral  :  4.701  18.379   1048
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    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:  0.73 (0.26), residues: 1031
  helix:  2.44 (0.30), residues: 277
  sheet: -0.43 (0.28), residues: 329
  loop :  0.06 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R 193 
 HIS   0.009   0.003   HIS R 300 
 PHE   0.016   0.001   PHE A  80 
 TYR   0.016   0.001   TYR R 144 
 ARG   0.002   0.001   ARG R 372 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.642 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 17
  average time/residue: 0.0620
  time to fit residues: 2.8151
Evaluate side-chains
  14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 66 optimal weight:   30.0000
   chunk 13 optimal weight:    7.9990
   chunk 57 optimal weight:   40.0000
   chunk 10 optimal weight:    7.9990
   chunk 50 optimal weight:    7.9990
   chunk 69 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 77 optimal weight:   20.0000
   chunk 99 optimal weight:   30.0000
   chunk 39 optimal weight:    5.9990
   chunk 2 optimal weight:    9.9990
   overall best weight:    6.9990

-------------------------------------------------------------------------------
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 = 0.2852 r_free = 0.2852 target = 0.035387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2512 r_free = 0.2512 target = 0.024107 restraints weight = 110416.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2513 r_free = 0.2513 target = 0.024121 restraints weight = 110179.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2513 r_free = 0.2513 target = 0.024121 restraints weight = 109489.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5636
moved from start:          0.6945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   5935  Z= 0.255
  Angle     :  0.596   7.450   8280  Z= 0.337
  Chirality :  0.041   0.164   1172
  Planarity :  0.005   0.056   1111
  Dihedral  :  5.122  23.757   1048
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    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:  0.30 (0.26), residues: 1031
  helix:  2.53 (0.31), residues: 280
  sheet: -0.98 (0.27), residues: 332
  loop : -0.28 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP R 193 
 HIS   0.008   0.003   HIS R 300 
 PHE   0.012   0.001   PHE A   9 
 TYR   0.016   0.001   TYR R 144 
 ARG   0.005   0.002   ARG R 372 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.645 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 17
  average time/residue: 0.0551
  time to fit residues: 2.6223
Evaluate side-chains
  14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 85 optimal weight:   10.0000
   chunk 92 optimal weight:    6.9990
   chunk 99 optimal weight:    0.4980
   chunk 2 optimal weight:    7.9990
   chunk 72 optimal weight:   10.0000
   chunk 77 optimal weight:   30.0000
   chunk 90 optimal weight:   10.0000
   chunk 67 optimal weight:    4.9990
   chunk 65 optimal weight:   50.0000
   chunk 38 optimal weight:    7.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:    5.0988

-------------------------------------------------------------------------------
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 = 0.2854 r_free = 0.2854 target = 0.035552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2516 r_free = 0.2516 target = 0.024237 restraints weight = 107695.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2516 r_free = 0.2516 target = 0.024237 restraints weight = 106947.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2516 r_free = 0.2516 target = 0.024237 restraints weight = 106947.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5620
moved from start:          0.7293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5935  Z= 0.180
  Angle     :  0.501   7.525   8280  Z= 0.274
  Chirality :  0.040   0.152   1172
  Planarity :  0.004   0.050   1111
  Dihedral  :  4.487  20.436   1048
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    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:  0.57 (0.27), residues: 1031
  helix:  2.99 (0.31), residues: 280
  sheet: -0.94 (0.28), residues: 326
  loop : -0.22 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP R 193 
 HIS   0.006   0.002   HIS R 300 
 PHE   0.012   0.001   PHE A   9 
 TYR   0.014   0.001   TYR R 144 
 ARG   0.002   0.001   ARG R 372 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.630 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 17
  average time/residue: 0.0592
  time to fit residues: 2.8349
Evaluate side-chains
  14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 55 optimal weight:   50.0000
   chunk 88 optimal weight:   40.0000
   chunk 14 optimal weight:    9.9990
   chunk 59 optimal weight:    3.9990
   chunk 25 optimal weight:    8.9990
   chunk 100 optimal weight:    7.9990
   chunk 86 optimal weight:   20.0000
   chunk 74 optimal weight:    8.9990
   chunk 96 optimal weight:   40.0000
   chunk 1 optimal weight:   30.0000
   chunk 58 optimal weight:   50.0000
   overall best weight:    7.9990

-------------------------------------------------------------------------------
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 = 0.2795 r_free = 0.2795 target = 0.033684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2465 r_free = 0.2465 target = 0.023040 restraints weight = 112991.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2466 r_free = 0.2466 target = 0.023082 restraints weight = 110783.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 14)----------------|
| r_work = 0.2466 r_free = 0.2466 target = 0.023082 restraints weight = 108970.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5776
moved from start:          0.8536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   5935  Z= 0.280
  Angle     :  0.609   7.338   8280  Z= 0.346
  Chirality :  0.041   0.148   1172
  Planarity :  0.005   0.048   1111
  Dihedral  :  5.393  24.597   1048
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 14.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    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:  0.00 (0.27), residues: 1031
  helix:  2.82 (0.30), residues: 272
  sheet: -1.30 (0.27), residues: 324
  loop : -0.70 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP R 193 
 HIS   0.007   0.003   HIS R 300 
 PHE   0.013   0.001   PHE A   9 
 TYR   0.016   0.001   TYR R 144 
 ARG   0.003   0.002   ARG R 372 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.680 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0585
  time to fit residues: 2.6767
Evaluate side-chains
  14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 74 optimal weight:    5.9990
   chunk 62 optimal weight:    9.9990
   chunk 60 optimal weight:   30.0000
   chunk 2 optimal weight:    7.9990
   chunk 16 optimal weight:   20.0000
   chunk 38 optimal weight:    5.9990
   chunk 43 optimal weight:   20.0000
   chunk 7 optimal weight:    9.9990
   chunk 84 optimal weight:   10.0000
   chunk 14 optimal weight:   20.0000
   overall best weight:    7.3990

-------------------------------------------------------------------------------
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 = 0.2800 r_free = 0.2800 target = 0.033605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2471 r_free = 0.2471 target = 0.023010 restraints weight = 113123.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2473 r_free = 0.2473 target = 0.023062 restraints weight = 110395.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2475 r_free = 0.2475 target = 0.023110 restraints weight = 107820.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5750
moved from start:          0.9060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5935  Z= 0.231
  Angle     :  0.548   7.476   8280  Z= 0.306
  Chirality :  0.040   0.149   1172
  Planarity :  0.005   0.049   1111
  Dihedral  :  5.131  22.926   1048
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    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: -0.06 (0.27), residues: 1031
  helix:  2.77 (0.30), residues: 279
  sheet: -1.37 (0.28), residues: 324
  loop : -0.78 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP R 193 
 HIS   0.006   0.003   HIS R 300 
 PHE   0.012   0.001   PHE A   9 
 TYR   0.014   0.001   TYR R 144 
 ARG   0.001   0.000   ARG R 372 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.710 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0581
  time to fit residues: 2.6038
Evaluate side-chains
  14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 27 optimal weight:   20.0000
   chunk 62 optimal weight:   20.0000
   chunk 58 optimal weight:   40.0000
   chunk 30 optimal weight:    6.9990
   chunk 26 optimal weight:    8.9990
   chunk 15 optimal weight:   20.0000
   chunk 99 optimal weight:    8.9990
   chunk 97 optimal weight:   50.0000
   chunk 43 optimal weight:   40.0000
   chunk 91 optimal weight:    4.9990
   chunk 47 optimal weight:    7.9990
   overall best weight:    7.5990

-------------------------------------------------------------------------------
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 = 0.2779 r_free = 0.2779 target = 0.033132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2455 r_free = 0.2455 target = 0.022765 restraints weight = 112178.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2457 r_free = 0.2457 target = 0.022810 restraints weight = 109550.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2459 r_free = 0.2459 target = 0.022864 restraints weight = 107329.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5790
moved from start:          0.9800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5935  Z= 0.255
  Angle     :  0.586   8.309   8280  Z= 0.330
  Chirality :  0.040   0.148   1172
  Planarity :  0.005   0.047   1111
  Dihedral  :  5.428  24.603   1048
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 14.72
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.37 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    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: -0.27 (0.27), residues: 1031
  helix:  2.85 (0.30), residues: 272
  sheet: -1.46 (0.29), residues: 318
  loop : -1.08 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP R 193 
 HIS   0.006   0.003   HIS R 300 
 PHE   0.012   0.001   PHE A   9 
 TYR   0.016   0.001   TYR R 144 
 ARG   0.003   0.002   ARG R 372 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.589 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0547
  time to fit residues: 2.4548
Evaluate side-chains
  14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 22 optimal weight:   50.0000
   chunk 54 optimal weight:    9.9990
   chunk 49 optimal weight:    9.9990
   chunk 76 optimal weight:    7.9990
   chunk 73 optimal weight:   20.0000
   chunk 81 optimal weight:   30.0000
   chunk 21 optimal weight:   20.0000
   chunk 80 optimal weight:    6.9990
   chunk 50 optimal weight:   40.0000
   chunk 61 optimal weight:   30.0000
   chunk 70 optimal weight:    7.9990
   overall best weight:    8.5990

-------------------------------------------------------------------------------
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 = 0.2770 r_free = 0.2770 target = 0.032908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2451 r_free = 0.2451 target = 0.022740 restraints weight = 114587.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2451 r_free = 0.2451 target = 0.022740 restraints weight = 110637.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2451 r_free = 0.2451 target = 0.022740 restraints weight = 110637.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5692
moved from start:          1.0421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5935  Z= 0.267
  Angle     :  0.599   8.332   8280  Z= 0.339
  Chirality :  0.041   0.139   1172
  Planarity :  0.005   0.049   1111
  Dihedral  :  5.644  24.531   1048
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 15.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.89 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    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: -0.61 (0.27), residues: 1031
  helix:  2.57 (0.30), residues: 276
  sheet: -1.68 (0.28), residues: 312
  loop : -1.32 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP R 193 
 HIS   0.006   0.003   HIS R 300 
 PHE   0.012   0.001   PHE A   9 
 TYR   0.015   0.001   TYR R 144 
 ARG   0.002   0.001   ARG R 372 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.656 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0670
  time to fit residues: 2.7091
Evaluate side-chains
  14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 43 optimal weight:    0.2980
   chunk 93 optimal weight:    9.9990
   chunk 81 optimal weight:   20.0000
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    9.9990
   chunk 91 optimal weight:   10.0000
   chunk 42 optimal weight:    5.9990
   chunk 59 optimal weight:    0.0370
   chunk 22 optimal weight:   40.0000
   chunk 2 optimal weight:    6.9990
   overall best weight:    4.6664

-------------------------------------------------------------------------------
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 = 0.2798 r_free = 0.2798 target = 0.033560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2469 r_free = 0.2469 target = 0.023012 restraints weight = 111076.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2469 r_free = 0.2469 target = 0.023012 restraints weight = 108038.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2469 r_free = 0.2469 target = 0.023012 restraints weight = 108038.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5740
moved from start:          1.0354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   5935  Z= 0.174
  Angle     :  0.509   8.150   8280  Z= 0.280
  Chirality :  0.040   0.141   1172
  Planarity :  0.005   0.052   1111
  Dihedral  :  4.925  22.550   1048
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    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: -0.22 (0.27), residues: 1031
  helix:  2.90 (0.30), residues: 280
  sheet: -1.55 (0.29), residues: 293
  loop : -1.07 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP R 193 
 HIS   0.006   0.003   HIS R 300 
 PHE   0.010   0.001   PHE A   9 
 TYR   0.014   0.001   TYR R 144 
 ARG   0.001   0.000   ARG R 372 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.703 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0555
  time to fit residues: 2.4453
Evaluate side-chains
  14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 7 optimal weight:    8.9990
   chunk 43 optimal weight:   40.0000
   chunk 26 optimal weight:    0.0970
   chunk 69 optimal weight:    4.9990
   chunk 56 optimal weight:    4.9990
   chunk 72 optimal weight:   10.0000
   chunk 80 optimal weight:    0.0470
   chunk 77 optimal weight:   30.0000
   chunk 46 optimal weight:    7.9990
   chunk 102 optimal weight:   30.0000
   chunk 64 optimal weight:   50.0000
   overall best weight:    3.6282

-------------------------------------------------------------------------------
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 = 0.2811 r_free = 0.2811 target = 0.033988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2478 r_free = 0.2478 target = 0.023212 restraints weight = 109565.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2479 r_free = 0.2479 target = 0.023255 restraints weight = 106626.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2480 r_free = 0.2480 target = 0.023262 restraints weight = 104586.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5712
moved from start:          1.0338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   5935  Z= 0.151
  Angle     :  0.477   7.945   8280  Z= 0.257
  Chirality :  0.040   0.138   1172
  Planarity :  0.004   0.054   1111
  Dihedral  :  4.408  20.999   1048
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    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: -0.01 (0.27), residues: 1031
  helix:  3.08 (0.31), residues: 286
  sheet: -1.49 (0.30), residues: 284
  loop : -0.99 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP R 193 
 HIS   0.005   0.002   HIS R 300 
 PHE   0.008   0.001   PHE A   9 
 TYR   0.012   0.001   TYR R 144 
 ARG   0.001   0.000   ARG R 372 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1769.61 seconds
wall clock time: 32 minutes 24.19 seconds (1944.19 seconds total)