Starting phenix.real_space_refine
on Wed Sep 17 05:20:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9g69_51096/09_2025/9g69_51096.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g69_51096/09_2025/9g69_51096.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g69_51096/09_2025/9g69_51096.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g69_51096/09_2025/9g69_51096.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9g69_51096/09_2025/9g69_51096.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g69_51096/09_2025/9g69_51096.map"
  }
  resolution = 4.84
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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
     P       3      5.49       5
     C    2976      2.51       5
     N    1033      2.21       5
     O    1041      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5053
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 1784
          Classifications: {'peptide': 366}
          Incomplete info: {'truncation_to_alanine': 288}
          Link IDs: {'PTRANS': 8, 'TRANS': 357}
          Unresolved chain link angles: 8
          Unresolved non-hydrogen bonds: 1003
          Unresolved non-hydrogen angles: 1286
          Unresolved non-hydrogen dihedrals: 808
          Unresolved non-hydrogen chiralities: 107
          Planarities with less than four sites: {'TYR:plan': 14, 'PHE:plan': 13, 'ASP:plan': 24, 'ARG:plan': 10, 'GLU:plan': 29, 'ASN:plan1': 16, 'GLN:plan1': 9, 'HIS:plan': 6}
          Unresolved non-hydrogen planarities: 528
    Chain: "B"
      Number of atoms: 1784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 1784
          Classifications: {'peptide': 366}
          Incomplete info: {'truncation_to_alanine': 288}
          Link IDs: {'PTRANS': 8, 'TRANS': 357}
          Unresolved chain link angles: 8
          Unresolved non-hydrogen bonds: 1003
          Unresolved non-hydrogen angles: 1286
          Unresolved non-hydrogen dihedrals: 808
          Unresolved non-hydrogen chiralities: 107
          Planarities with less than four sites: {'TYR:plan': 14, 'PHE:plan': 13, 'ASP:plan': 24, 'ARG:plan': 10, 'GLU:plan': 29, 'ASN:plan1': 16, 'GLN:plan1': 9, 'HIS:plan': 6}
          Unresolved non-hydrogen planarities: 528
    Chain: "C"
      Number of atoms: 732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 149, 732
          Classifications: {'peptide': 149}
          Incomplete info: {'truncation_to_alanine': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 145}
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 418
          Unresolved non-hydrogen angles: 534
          Unresolved non-hydrogen dihedrals: 338
          Unresolved non-hydrogen chiralities: 48
          Planarities with less than four sites: {'ASP:plan': 7, 'HIS:plan': 5, 'TYR:plan': 3, 'GLU:plan': 11, 'PHE:plan': 7, 'ARG:plan': 5, 'GLN:plan1': 3, 'ASN:plan1': 6}
          Unresolved non-hydrogen planarities: 208
    Chain: "D"
      Number of atoms: 722
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 722
          Classifications: {'peptide': 147}
          Incomplete info: {'truncation_to_alanine': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 143}
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 410
          Unresolved non-hydrogen angles: 526
          Unresolved non-hydrogen dihedrals: 330
          Unresolved non-hydrogen chiralities: 48
          Planarities with less than four sites: {'ASP:plan': 7, 'HIS:plan': 5, 'TYR:plan': 3, 'GLU:plan': 11, 'PHE:plan': 7, 'ARG:plan': 5, 'GLN:plan1': 3, 'ASN:plan1': 6}
          Unresolved non-hydrogen planarities: 208
    Chain: "D"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.49, per 1000 atoms: 0.29
  Number of scatterers: 5053
  At special positions: 0
  Unit cell: (80.738, 88.914, 118.552, 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)
     P       3     15.00
     O    1041      8.00
     N    1033      7.00
     C    2976      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.40
  Conformation dependent library (CDL) restraints added in 236.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1820

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 9 sheets defined
      41.0% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 36
      removed outlier: 3.715A  pdb=" N   GLY A  30 " --> pdb=" O   LEU A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 66
      removed outlier: 4.197A  pdb=" N   LEU A  57 " --> pdb=" O   SER A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 91
      removed outlier: 3.884A  pdb=" N   GLY A  91 " --> pdb=" O   VAL A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 134
    Processing helix  chain 'A' and resid 155 through 167
      removed outlier: 3.679A  pdb=" N   LYS A 159 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   TYR A 160 " --> pdb=" O   GLY A 156 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU A 164 " --> pdb=" O   TYR A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 188
      removed outlier: 3.791A  pdb=" N   THR A 188 " --> pdb=" O   ALA A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 197
    Processing helix  chain 'A' and resid 222 through 233
    Processing helix  chain 'A' and resid 258 through 274
      removed outlier: 3.632A  pdb=" N   GLN A 273 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 299
      removed outlier: 3.871A  pdb=" N   HIS A 292 " --> pdb=" O   ASN A 288 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU A 293 " --> pdb=" O   LEU A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 320
    Processing helix  chain 'A' and resid 341 through 356
    Processing helix  chain 'A' and resid 359 through 364
      removed outlier: 3.858A  pdb=" N   LEU A 363 " --> pdb=" O   SER A 359 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   ALA A 364 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 359 through 364'
    Processing helix  chain 'B' and resid 19 through 35
      removed outlier: 4.022A  pdb=" N   ARG B  28 " --> pdb=" O   PHE B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 69
      removed outlier: 3.580A  pdb=" N   GLN B  55 " --> pdb=" O   ARG B  51 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   MET B  56 " --> pdb=" O   ILE B  52 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU B  66 " --> pdb=" O   ILE B  62 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   SER B  67 " --> pdb=" O   SER B  63 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   VAL B  68 " --> pdb=" O   GLY B  64 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLY B  69 " --> pdb=" O   LEU B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 91
    Processing helix  chain 'B' and resid 121 through 134
      removed outlier: 3.747A  pdb=" N   GLU B 125 " --> pdb=" O   GLU B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 169
      removed outlier: 3.701A  pdb=" N   TYR B 160 " --> pdb=" O   GLY B 156 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU B 164 " --> pdb=" O   TYR B 160 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLU B 169 " --> pdb=" O   LYS B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 197
    Processing helix  chain 'B' and resid 222 through 232
      removed outlier: 3.533A  pdb=" N   ALA B 226 " --> pdb=" O   PRO B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 273
    Processing helix  chain 'B' and resid 288 through 299
    Processing helix  chain 'B' and resid 308 through 319
    Processing helix  chain 'B' and resid 341 through 357
    Processing helix  chain 'C' and resid 119 through 138
      removed outlier: 3.579A  pdb=" N   SER C 127 " --> pdb=" O   ASP C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 168 through 176
    Processing helix  chain 'C' and resid 214 through 226
      removed outlier: 3.991A  pdb=" N   ARG C 218 " --> pdb=" O   GLY C 214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 254 through 265
    Processing helix  chain 'D' and resid 124 through 139
    Processing helix  chain 'D' and resid 168 through 176
    Processing helix  chain 'D' and resid 214 through 221
    Processing helix  chain 'D' and resid 222 through 227
      removed outlier: 3.928A  pdb=" N   VAL D 226 " --> pdb=" O   GLY D 222 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 254 through 266
    Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12
      removed outlier: 3.860A  pdb=" N   GLY A  12 " --> pdb=" O   ASN A 108 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 204
      removed outlier: 3.532A  pdb=" N   THR A 202 " --> pdb=" O   VAL A 177 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   PHE A 240 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
      removed outlier: 5.081A  pdb=" N   VAL A 250 " --> pdb=" O   GLY A 237 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ILE A 248 " --> pdb=" O   ALA A 239 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ALA A 249 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 6
      removed outlier: 3.810A  pdb=" N   GLY B   9 " --> pdb=" O   GLY B   6 " (cutoff:3.500A)
      removed outlier: 7.155A  pdb=" N   LYS B  43 " --> pdb=" O   ALA B  94 " (cutoff:3.500A)
      removed outlier: 9.027A  pdb=" N   VAL B  96 " --> pdb=" O   LYS B  43 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   TYR B  45 " --> pdb=" O   VAL B  96 " (cutoff:3.500A)
      removed outlier: 8.434A  pdb=" N   ILE B  98 " --> pdb=" O   TYR B  45 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   GLY B  47 " --> pdb=" O   ILE B  98 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   TYR B  73 " --> pdb=" O   VAL B  44 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   VAL B  46 " --> pdb=" O   TYR B  73 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   VAL B  72 " --> pdb=" O   HIS B 151 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 177 through 178
      removed outlier: 6.118A  pdb=" N   VAL B 178 " --> pdb=" O   LEU B 238 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 280 through 284
      removed outlier: 3.798A  pdb=" N   VAL B 303 " --> pdb=" O   LEU B 281 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR B 305 " --> pdb=" O   THR B 283 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 325
    Processing sheet with id=AA7, first strand: chain 'C' and resid 189 through 190
    Processing sheet with id=AA8, first strand: chain 'C' and resid 230 through 234
      removed outlier: 3.899A  pdb=" N   ALA C 244 " --> pdb=" O   ILE C 231 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   VAL C 233 " --> pdb=" O   SER C 242 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   SER C 242 " --> pdb=" O   VAL C 233 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 193 through 194
      removed outlier: 3.682A  pdb=" N   VAL D 187 " --> pdb=" O   LEU D 144 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ALA D 143 " --> pdb=" O   VAL D 234 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL D 234 " --> pdb=" O   ALA D 143 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   VAL D 233 " --> pdb=" O   SER D 242 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   SER D 242 " --> pdb=" O   VAL D 233 " (cutoff:3.500A)

    313 hydrogen bonds defined for protein.
    903 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.78

  Time building geometry restraints manager: 0.53 seconds

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

  Histogram of bond lengths:
        1.23 -     1.30: 1028
        1.30 -     1.38: 1033
        1.38 -     1.46: 458
        1.46 -     1.53: 2349
        1.53 -     1.61: 183
  Bond restraints: 5051
  Sorted by residual:
  bond pdb=" O5' ATP D 301 "
       pdb=" PA  ATP D 301 "
    ideal  model  delta    sigma   weight residual
    1.579  1.604 -0.025 1.10e-02 8.26e+03 5.22e+00
  bond pdb=" O2A ATP D 301 "
       pdb=" PA  ATP D 301 "
    ideal  model  delta    sigma   weight residual
    1.529  1.492  0.037 2.20e-02 2.07e+03 2.76e+00
  bond pdb=" O2B ATP D 301 "
       pdb=" PB  ATP D 301 "
    ideal  model  delta    sigma   weight residual
    1.529  1.493  0.036 2.20e-02 2.07e+03 2.75e+00
  bond pdb=" O1A ATP D 301 "
       pdb=" PA  ATP D 301 "
    ideal  model  delta    sigma   weight residual
    1.477  1.492 -0.015 1.10e-02 8.26e+03 1.87e+00
  bond pdb=" C4  ATP D 301 "
       pdb=" C5  ATP D 301 "
    ideal  model  delta    sigma   weight residual
    1.388  1.377  0.011 1.00e-02 1.00e+04 1.15e+00
  ... (remaining 5046 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.30: 6685
        1.30 -     2.61: 270
        2.61 -     3.91: 30
        3.91 -     5.22: 10
        5.22 -     6.52: 5
  Bond angle restraints: 7000
  Sorted by residual:
  angle pdb=" PB  ATP D 301 "
        pdb=" O3B ATP D 301 "
        pdb=" PG  ATP D 301 "
      ideal   model   delta    sigma   weight residual
     139.87  133.98    5.89 1.00e+00 1.00e+00 3.46e+01
  angle pdb=" CA  THR B  80 "
        pdb=" C   THR B  80 "
        pdb=" N   PRO B  81 "
      ideal   model   delta    sigma   weight residual
     120.93  117.52    3.41 1.06e+00 8.90e-01 1.03e+01
  angle pdb=" C   GLN A 278 "
        pdb=" N   ASP A 279 "
        pdb=" CA  ASP A 279 "
      ideal   model   delta    sigma   weight residual
     121.54  127.61   -6.07 1.91e+00 2.74e-01 1.01e+01
  angle pdb=" C   VAL C 157 "
        pdb=" CA  VAL C 157 "
        pdb=" CB  VAL C 157 "
      ideal   model   delta    sigma   weight residual
     111.88  107.73    4.15 1.37e+00 5.33e-01 9.16e+00
  angle pdb=" N   ALA C 229 "
        pdb=" CA  ALA C 229 "
        pdb=" C   ALA C 229 "
      ideal   model   delta    sigma   weight residual
     110.43  114.32   -3.89 1.31e+00 5.83e-01 8.83e+00
  ... (remaining 6995 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.02: 2851
       17.02 -    34.03: 14
       34.03 -    51.05: 4
       51.05 -    68.07: 7
       68.07 -    85.08: 2
  Dihedral angle restraints: 2878
    sinusoidal: 34
      harmonic: 2844
  Sorted by residual:
  dihedral pdb=" CA  GLN A 278 "
           pdb=" C   GLN A 278 "
           pdb=" N   ASP A 279 "
           pdb=" CA  ASP A 279 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.77  -25.23     0      5.00e+00 4.00e-02 2.55e+01
  dihedral pdb=" CA  LEU C 230 "
           pdb=" C   LEU C 230 "
           pdb=" N   ILE C 231 "
           pdb=" CA  ILE C 231 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.58  -19.42     0      5.00e+00 4.00e-02 1.51e+01
  dihedral pdb=" CA  HIS C 245 "
           pdb=" C   HIS C 245 "
           pdb=" N   ASN C 246 "
           pdb=" CA  ASN C 246 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.45   18.55     0      5.00e+00 4.00e-02 1.38e+01
  ... (remaining 2875 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 476
       0.029 -    0.057: 251
       0.057 -    0.086: 106
       0.086 -    0.114: 68
       0.114 -    0.143: 13
  Chirality restraints: 914
  Sorted by residual:
  chirality pdb=" CA  ILE A  78 "
            pdb=" N   ILE A  78 "
            pdb=" C   ILE A  78 "
            pdb=" CB  ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.10e-01
  chirality pdb=" CA  ILE D 147 "
            pdb=" N   ILE D 147 "
            pdb=" C   ILE D 147 "
            pdb=" CB  ILE D 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.24e-01
  chirality pdb=" CA  ILE C 147 "
            pdb=" N   ILE C 147 "
            pdb=" C   ILE C 147 "
            pdb=" CB  ILE C 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.13e-01
  ... (remaining 911 not shown)

  Planarity restraints: 1025
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D 122 "    0.005 2.00e-02 2.50e+03   9.43e-03 8.89e-01
        pdb=" C   LEU D 122 "   -0.016 2.00e-02 2.50e+03
        pdb=" O   LEU D 122 "    0.006 2.00e-02 2.50e+03
        pdb=" N   ASP D 123 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 109 "   -0.005 2.00e-02 2.50e+03   9.41e-03 8.85e-01
        pdb=" C   GLY A 109 "    0.016 2.00e-02 2.50e+03
        pdb=" O   GLY A 109 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   ILE A 110 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 280 "   -0.005 2.00e-02 2.50e+03   9.21e-03 8.48e-01
        pdb=" C   THR B 280 "    0.016 2.00e-02 2.50e+03
        pdb=" O   THR B 280 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   LEU B 281 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1022 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 2152
        2.89 -     3.39: 4675
        3.39 -     3.89: 7162
        3.89 -     4.40: 6962
        4.40 -     4.90: 11852
  Nonbonded interactions: 32803
  Sorted by model distance:
  nonbonded pdb=" O   ILE C 188 "
            pdb=" N   ALA C 195 "
     model   vdw
     2.386 3.120
  nonbonded pdb=" O   ALA A 244 "
            pdb=" N   GLY A 342 "
     model   vdw
     2.396 3.120
  nonbonded pdb=" N   ASP A  49 "
            pdb=" O   ILE A  98 "
     model   vdw
     2.457 3.120
  nonbonded pdb=" O   LEU C 153 "
            pdb=" N   VAL C 157 "
     model   vdw
     2.475 3.120
  nonbonded pdb=" O   GLY B  95 "
            pdb=" N   PHE B 113 "
     model   vdw
     2.484 3.120
  ... (remaining 32798 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = (chain 'C' and resid 120 through 266)
  selection = (chain 'D' and resid 120 through 266)
}

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:             1.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.670
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6871
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      :  0.002   0.037   5051  Z= 0.167
  Angle     :  0.620   6.524   7000  Z= 0.401
  Chirality :  0.046   0.143    914
  Planarity :  0.002   0.009   1025
  Dihedral  :  8.653  85.084   1058
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.65 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.18 (0.26), residues: 1020
  helix: -0.37 (0.24), residues: 391
  sheet: -2.58 (0.43), residues: 129
  loop : -2.00 (0.29), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A   4 
 PHE   0.000   0.000   PHE A   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 5051)
  covalent geometry    : angle       0.62006 ( 7000)
  hydrogen bonds       : bond        0.17133 (  313)
  hydrogen bonds       : angle       7.71077 (  903)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.169 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0235
  time to fit residues: 1.2813
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   overall best weight:    2.5586

-------------------------------------------------------------------------------
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 = 0.3768 r_free = 0.3768 target = 0.149945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.130806 restraints weight = 115904.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.133446 restraints weight = 87282.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.134462 restraints weight = 71428.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.135002 restraints weight = 70120.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.135528 restraints weight = 65129.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6950
moved from start:          0.1068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5051  Z= 0.185
  Angle     :  0.542   4.609   7000  Z= 0.336
  Chirality :  0.046   0.128    914
  Planarity :  0.003   0.012   1025
  Dihedral  :  7.955  85.907   1058
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 12.06 %
    Favored  : 87.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.68 (0.27), residues: 1020
  helix:  0.58 (0.26), residues: 402
  sheet: -2.77 (0.46), residues: 107
  loop : -2.19 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A   4 
 PHE   0.000   0.000   PHE A   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 5051)
  covalent geometry    : angle       0.54178 ( 7000)
  hydrogen bonds       : bond        0.04239 (  313)
  hydrogen bonds       : angle       6.08690 (  903)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.173 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0238
  time to fit residues: 1.2933
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 74 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 64 optimal weight:   20.0000
   chunk 17 optimal weight:    9.9990
   chunk 36 optimal weight:    9.9990
   chunk 96 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 79 optimal weight:   10.0000
   chunk 32 optimal weight:    0.6980
   chunk 68 optimal weight:    7.9990
   chunk 90 optimal weight:    7.9990
   overall best weight:    5.7388

-------------------------------------------------------------------------------
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 = 0.3617 r_free = 0.3617 target = 0.137860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.120394 restraints weight = 120705.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.122924 restraints weight = 93514.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.123578 restraints weight = 75994.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.124361 restraints weight = 70099.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.124769 restraints weight = 66804.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7159
moved from start:          0.2301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   5051  Z= 0.370
  Angle     :  0.831   7.725   7000  Z= 0.520
  Chirality :  0.050   0.152    914
  Planarity :  0.005   0.019   1025
  Dihedral  :  8.991  88.894   1058
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 17.45 %
    Favored  : 82.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.26 (0.25), residues: 1020
  helix: -0.81 (0.24), residues: 400
  sheet: -2.75 (0.53), residues: 86
  loop : -3.27 (0.25), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A   4 
 PHE   0.000   0.000   PHE A   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 ( 5051)
  covalent geometry    : angle       0.83106 ( 7000)
  hydrogen bonds       : bond        0.06804 (  313)
  hydrogen bonds       : angle       8.05500 (  903)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.211 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0169
  time to fit residues: 0.9691
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 77 optimal weight:    7.9990
   chunk 18 optimal weight:   10.0000
   chunk 39 optimal weight:    0.0060
   chunk 12 optimal weight:    4.9990
   chunk 93 optimal weight:   10.0000
   chunk 9 optimal weight:    7.9990
   chunk 87 optimal weight:    8.9990
   chunk 42 optimal weight:   10.0000
   chunk 60 optimal weight:   10.0000
   chunk 71 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    4.2004

-------------------------------------------------------------------------------
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 = 0.3645 r_free = 0.3645 target = 0.140439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.122855 restraints weight = 120969.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.125149 restraints weight = 94130.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.125542 restraints weight = 80252.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.126322 restraints weight = 76006.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.126847 restraints weight = 68016.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5051  Z= 0.272
  Angle     :  0.685   6.432   7000  Z= 0.427
  Chirality :  0.048   0.138    914
  Planarity :  0.004   0.016   1025
  Dihedral  :  8.418  89.889   1058
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 16.76 %
    Favored  : 83.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.13 (0.25), residues: 1020
  helix: -0.53 (0.25), residues: 397
  sheet: -3.09 (0.51), residues: 96
  loop : -3.23 (0.26), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A   4 
 PHE   0.000   0.000   PHE A   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 5051)
  covalent geometry    : angle       0.68509 ( 7000)
  hydrogen bonds       : bond        0.05389 (  313)
  hydrogen bonds       : angle       7.19981 (  903)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.188 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0234
  time to fit residues: 1.2972
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 55 optimal weight:    7.9990
   chunk 40 optimal weight:    2.9990
   chunk 78 optimal weight:    0.2980
   chunk 81 optimal weight:    0.0980
   chunk 26 optimal weight:    9.9990
   chunk 70 optimal weight:    5.9990
   chunk 61 optimal weight:    9.9990
   chunk 56 optimal weight:   10.0000
   chunk 66 optimal weight:   40.0000
   chunk 33 optimal weight:    9.9990
   chunk 7 optimal weight:    9.9990
   overall best weight:    3.4786

-------------------------------------------------------------------------------
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 = 0.3661 r_free = 0.3661 target = 0.141789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.123791 restraints weight = 120034.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.126267 restraints weight = 93183.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.127192 restraints weight = 75839.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.127891 restraints weight = 73052.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.128269 restraints weight = 67550.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
moved from start:          0.2578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5051  Z= 0.235
  Angle     :  0.626   5.714   7000  Z= 0.390
  Chirality :  0.047   0.136    914
  Planarity :  0.003   0.014   1025
  Dihedral  :  8.072  87.584   1058
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 17.45 %
    Favored  : 82.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.86 (0.26), residues: 1020
  helix: -0.20 (0.26), residues: 391
  sheet: -3.07 (0.51), residues: 96
  loop : -3.11 (0.26), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A   4 
 PHE   0.000   0.000   PHE A   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 5051)
  covalent geometry    : angle       0.62562 ( 7000)
  hydrogen bonds       : bond        0.04753 (  313)
  hydrogen bonds       : angle       6.69099 (  903)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.166 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0218
  time to fit residues: 1.1933
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    5.9990
   chunk 1 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   chunk 92 optimal weight:   10.0000
   chunk 51 optimal weight:   20.0000
   chunk 90 optimal weight:    9.9990
   chunk 85 optimal weight:    9.9990
   chunk 80 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 78 optimal weight:    6.9990
   chunk 63 optimal weight:    7.9990
   overall best weight:    8.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.130324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.113760 restraints weight = 124442.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.115544 restraints weight = 97024.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.116641 restraints weight = 81394.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.117743 restraints weight = 74014.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.118442 restraints weight = 68049.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.3860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.063   5051  Z= 0.507
  Angle     :  1.044   9.506   7000  Z= 0.655
  Chirality :  0.054   0.162    914
  Planarity :  0.006   0.025   1025
  Dihedral  : 10.383  87.274   1058
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  : 23.92 %
    Favored  : 75.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.40 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.48 (0.23), residues: 1020
  helix: -1.86 (0.23), residues: 380
  sheet: -3.15 (0.56), residues: 70
  loop : -3.93 (0.23), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A   4 
 PHE   0.000   0.000   PHE A   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00713 ( 5051)
  covalent geometry    : angle       1.04424 ( 7000)
  hydrogen bonds       : bond        0.08704 (  313)
  hydrogen bonds       : angle       9.58903 (  903)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.174 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0251
  time to fit residues: 1.3288
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 31 optimal weight:    6.9990
   chunk 93 optimal weight:   10.0000
   chunk 41 optimal weight:    0.7980
   chunk 90 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 24 optimal weight:    9.9990
   chunk 72 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    2.1386

-------------------------------------------------------------------------------
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 = 0.3669 r_free = 0.3669 target = 0.142495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.125037 restraints weight = 118136.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.127634 restraints weight = 90577.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.128325 restraints weight = 73395.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.129028 restraints weight = 70287.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.129447 restraints weight = 66267.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7074
moved from start:          0.3133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5051  Z= 0.169
  Angle     :  0.582   6.014   7000  Z= 0.358
  Chirality :  0.046   0.132    914
  Planarity :  0.003   0.024   1025
  Dihedral  :  8.267  86.734   1058
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.84 %
    Favored  : 86.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.16 (0.26), residues: 1020
  helix: -0.35 (0.26), residues: 385
  sheet: -3.30 (0.52), residues: 91
  loop : -3.35 (0.25), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A   4 
 PHE   0.000   0.000   PHE A   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 5051)
  covalent geometry    : angle       0.58227 ( 7000)
  hydrogen bonds       : bond        0.04325 (  313)
  hydrogen bonds       : angle       6.65204 (  903)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.179 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0239
  time to fit residues: 1.2903
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 69 optimal weight:    8.9990
   chunk 57 optimal weight:    2.9990
   chunk 11 optimal weight:    9.9990
   chunk 10 optimal weight:    6.9990
   chunk 40 optimal weight:    7.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:   20.0000
   chunk 13 optimal weight:    5.9990
   chunk 38 optimal weight:    7.9990
   chunk 70 optimal weight:    9.9990
   chunk 37 optimal weight:    7.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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 = 0.3576 r_free = 0.3576 target = 0.134006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.116578 restraints weight = 123967.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.118912 restraints weight = 93672.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.119214 restraints weight = 80213.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.119979 restraints weight = 77673.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.121685 restraints weight = 71683.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7240
moved from start:          0.3691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   5051  Z= 0.361
  Angle     :  0.818   6.946   7000  Z= 0.513
  Chirality :  0.050   0.149    914
  Planarity :  0.005   0.020   1025
  Dihedral  :  9.303  85.008   1058
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 23.14 %
    Favored  : 76.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.30 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.01 (0.24), residues: 1020
  helix: -1.24 (0.25), residues: 381
  sheet: -3.36 (0.50), residues: 93
  loop : -3.75 (0.24), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A   4 
 PHE   0.000   0.000   PHE A   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 ( 5051)
  covalent geometry    : angle       0.81846 ( 7000)
  hydrogen bonds       : bond        0.06815 (  313)
  hydrogen bonds       : angle       8.30113 (  903)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.172 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0235
  time to fit residues: 1.2868
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 90 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 70 optimal weight:    9.9990
   chunk 42 optimal weight:    9.9990
   chunk 69 optimal weight:   10.0000
   chunk 26 optimal weight:   10.0000
   chunk 77 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 36 optimal weight:    9.9990
   chunk 56 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   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 = 0.3533 r_free = 0.3533 target = 0.130593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.114087 restraints weight = 125063.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.116462 restraints weight = 96943.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.117239 restraints weight = 78198.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.118088 restraints weight = 75041.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.118339 restraints weight = 70090.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.4242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061   5051  Z= 0.454
  Angle     :  0.955   8.087   7000  Z= 0.599
  Chirality :  0.053   0.154    914
  Planarity :  0.006   0.023   1025
  Dihedral  : 10.221  82.105   1058
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 23.63 %
    Favored  : 76.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.40 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.65 (0.23), residues: 1020
  helix: -1.96 (0.23), residues: 378
  sheet: -3.38 (0.57), residues: 76
  loop : -4.04 (0.22), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A   4 
 PHE   0.000   0.000   PHE A   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00638 ( 5051)
  covalent geometry    : angle       0.95550 ( 7000)
  hydrogen bonds       : bond        0.08040 (  313)
  hydrogen bonds       : angle       9.24980 (  903)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.179 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0233
  time to fit residues: 1.2688
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 49 optimal weight:    9.9990
   chunk 40 optimal weight:    9.9990
   chunk 73 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 37 optimal weight:   10.0000
   chunk 23 optimal weight:    7.9990
   chunk 24 optimal weight:   10.0000
   chunk 4 optimal weight:   20.0000
   chunk 78 optimal weight:    7.9990
   chunk 84 optimal weight:    8.9990
   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 = 0.3505 r_free = 0.3505 target = 0.128005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.111980 restraints weight = 128359.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.113606 restraints weight = 100105.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.114539 restraints weight = 84267.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.115205 restraints weight = 78380.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.115935 restraints weight = 73159.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7347
moved from start:          0.4813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.066   5051  Z= 0.484
  Angle     :  0.993   8.306   7000  Z= 0.625
  Chirality :  0.054   0.159    914
  Planarity :  0.006   0.027   1025
  Dihedral  : 10.696  74.661   1058
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 28.63 %
    Favored  : 71.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.70 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.12 (0.22), residues: 1020
  helix: -2.29 (0.23), residues: 371
  sheet: -3.48 (0.56), residues: 70
  loop : -4.38 (0.21), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A   4 
 PHE   0.000   0.000   PHE A   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00680 ( 5051)
  covalent geometry    : angle       0.99320 ( 7000)
  hydrogen bonds       : bond        0.08592 (  313)
  hydrogen bonds       : angle       9.72546 (  903)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.171 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0230
  time to fit residues: 1.2594
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 33 optimal weight:    0.0770
   chunk 60 optimal weight:   10.0000
   chunk 8 optimal weight:    3.9990
   chunk 11 optimal weight:   10.0000
   chunk 86 optimal weight:    9.9990
   chunk 96 optimal weight:    0.0050
   chunk 16 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   chunk 4 optimal weight:   20.0000
   chunk 10 optimal weight:    4.9990
   chunk 89 optimal weight:    8.9990
   overall best weight:    1.9756

-------------------------------------------------------------------------------
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 = 0.3667 r_free = 0.3667 target = 0.142212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.125348 restraints weight = 119706.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.126973 restraints weight = 93921.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.128399 restraints weight = 75785.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.129513 restraints weight = 69815.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.129963 restraints weight = 64653.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7070
moved from start:          0.4057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   5051  Z= 0.165
  Angle     :  0.563   5.452   7000  Z= 0.348
  Chirality :  0.046   0.135    914
  Planarity :  0.003   0.022   1025
  Dihedral  :  8.091  72.722   1058
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.25 %
    Favored  : 87.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.75 (0.25), residues: 1020
  helix: -0.67 (0.26), residues: 388
  sheet: -3.81 (0.52), residues: 80
  loop : -3.84 (0.23), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A   4 
 PHE   0.000   0.000   PHE A   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 5051)
  covalent geometry    : angle       0.56273 ( 7000)
  hydrogen bonds       : bond        0.04177 (  313)
  hydrogen bonds       : angle       6.67056 (  903)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 673.58 seconds
wall clock time: 12 minutes 15.67 seconds (735.67 seconds total)