Starting phenix.real_space_refine
on Fri Aug 22 17:41:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ge6_29958/08_2025/8ge6_29958.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ge6_29958/08_2025/8ge6_29958.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ge6_29958/08_2025/8ge6_29958.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ge6_29958/08_2025/8ge6_29958.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ge6_29958/08_2025/8ge6_29958.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ge6_29958/08_2025/8ge6_29958.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.032
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      40      5.16       5
     C    4220      2.51       5
     N    1131      2.21       5
     O    1169      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6560
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1731
          Classifications: {'peptide': 232}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 50}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 197
          Unresolved non-hydrogen angles: 237
          Unresolved non-hydrogen dihedrals: 160
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 7, 'ASN:plan1': 1, 'GLU:plan': 13, 'ASP:plan': 9, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 135
    Chain: "B"
      Number of atoms: 2405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2405
          Classifications: {'peptide': 331}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 5, 'TRANS': 325}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 139
          Unresolved non-hydrogen angles: 169
          Unresolved non-hydrogen dihedrals: 109
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 8, 'GLU:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 9}
          Unresolved non-hydrogen planarities: 109
    Chain: "G"
      Number of atoms: 349
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 349
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 65
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "R"
      Number of atoms: 2059
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2059
          Classifications: {'peptide': 277}
          Incomplete info: {'truncation_to_alanine': 50}
          Link IDs: {'PTRANS': 7, 'TRANS': 269}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 166
          Unresolved non-hydrogen angles: 201
          Unresolved non-hydrogen dihedrals: 133
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 3, 'GLN:plan1': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 87
    Chain: "R"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 16
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 1.29, per 1000 atoms: 0.20
  Number of scatterers: 6560
  At special positions: 0
  Unit cell: (69.96, 98.58, 129.32, 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      40     16.00
     O    1169      8.00
     N    1131      7.00
     C    4220      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.55
  Conformation dependent library (CDL) restraints added in 264.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1688

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 8 sheets defined
      47.5% alpha, 18.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 40
    Processing helix  chain 'A' and resid 52 through 58
      removed outlier: 3.524A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 238
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.946A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.639A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 7 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 12 through 22
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'R' and resid 36 through 61
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 3.701A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 4.950A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 4.401A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   SER R 143 " --> pdb=" O   PHE R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.530A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 237
    Processing helix  chain 'R' and resid 270 through 299
      removed outlier: 3.684A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.801A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 327
      removed outlier: 3.784A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 340
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.352A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.397A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.660A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.365A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.876A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 4.581A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.747A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.826A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.078A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.975A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.819A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.021A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.255A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.410A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.708A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.997A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278
      removed outlier: 6.676A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.822A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    383 hydrogen bonds defined for protein.
    1122 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: 0.74

  Time building geometry restraints manager: 0.73 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2121
        1.34 -     1.46: 1429
        1.46 -     1.58: 3096
        1.58 -     1.69: 0
        1.69 -     1.81: 55
  Bond restraints: 6701
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.449 -0.052 2.00e-02 2.50e+03 6.79e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.570 -0.047 2.00e-02 2.50e+03 5.45e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.565 -0.045 2.00e-02 2.50e+03 5.02e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.439 -0.045 2.00e-02 2.50e+03 5.02e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" NAN G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.451  1.485 -0.034 2.00e-02 2.50e+03 2.81e+00
  ... (remaining 6696 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 8975
        1.39 -     2.78: 145
        2.78 -     4.18: 25
        4.18 -     5.57: 10
        5.57 -     6.96: 2
  Bond angle restraints: 9157
  Sorted by residual:
  angle pdb=" N   GLU R 225 "
        pdb=" CA  GLU R 225 "
        pdb=" CB  GLU R 225 "
      ideal   model   delta    sigma   weight residual
     110.16  114.08   -3.92 1.48e+00 4.57e-01 7.01e+00
  angle pdb=" N   GLY A 329 "
        pdb=" CA  GLY A 329 "
        pdb=" C   GLY A 329 "
      ideal   model   delta    sigma   weight residual
     113.18  107.04    6.14 2.37e+00 1.78e-01 6.72e+00
  angle pdb=" CA  GLU A  50 "
        pdb=" CB  GLU A  50 "
        pdb=" CG  GLU A  50 "
      ideal   model   delta    sigma   weight residual
     114.10  118.67   -4.57 2.00e+00 2.50e-01 5.22e+00
  angle pdb=" CA  LEU A  46 "
        pdb=" CB  LEU A  46 "
        pdb=" CG  LEU A  46 "
      ideal   model   delta    sigma   weight residual
     116.30  123.26   -6.96 3.50e+00 8.16e-02 3.96e+00
  angle pdb=" C   THR R  96 "
        pdb=" N   LYS R  97 "
        pdb=" CA  LYS R  97 "
      ideal   model   delta    sigma   weight residual
     124.31  127.60   -3.29 1.67e+00 3.59e-01 3.88e+00
  ... (remaining 9152 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.94: 3459
       13.94 -    27.89: 309
       27.89 -    41.83: 100
       41.83 -    55.77: 10
       55.77 -    69.72: 6
  Dihedral angle restraints: 3884
    sinusoidal: 1284
      harmonic: 2600
  Sorted by residual:
  dihedral pdb=" CB  CYS R 106 "
           pdb=" SG  CYS R 106 "
           pdb=" SG  CYS R 191 "
           pdb=" CB  CYS R 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -145.70   59.70     1      1.00e+01 1.00e-02 4.76e+01
  dihedral pdb=" CB  MET G  38 "
           pdb=" CG  MET G  38 "
           pdb=" SD  MET G  38 "
           pdb=" CE  MET G  38 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  118.04  -58.04     3      1.50e+01 4.44e-03 9.46e+00
  dihedral pdb=" CA  PHE R 208 "
           pdb=" C   PHE R 208 "
           pdb=" N   TYR R 209 "
           pdb=" CA  TYR R 209 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.04  -14.96     0      5.00e+00 4.00e-02 8.95e+00
  ... (remaining 3881 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 711
       0.031 -    0.061: 246
       0.061 -    0.092: 83
       0.092 -    0.123: 48
       0.123 -    0.154: 6
  Chirality restraints: 1094
  Sorted by residual:
  chirality pdb=" CA  ASP B 291 "
            pdb=" N   ASP B 291 "
            pdb=" C   ASP B 291 "
            pdb=" CB  ASP B 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.89e-01
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.55   -0.15 2.00e-01 2.50e+01 5.80e-01
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.30e-01
  ... (remaining 1091 not shown)

  Planarity restraints: 1153
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL G  54 "   -0.031 5.00e-02 4.00e+02   4.74e-02 3.59e+00
        pdb=" N   PRO G  55 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO G  55 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO G  55 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER R 329 "   -0.028 5.00e-02 4.00e+02   4.34e-02 3.01e+00
        pdb=" N   PRO R 330 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO R 330 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO R 330 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "   -0.014 2.00e-02 2.50e+03   1.18e-02 2.77e+00
        pdb=" CG  TYR B  59 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1150 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1049
        2.76 -     3.29: 6405
        3.29 -     3.83: 11190
        3.83 -     4.36: 12467
        4.36 -     4.90: 22671
  Nonbonded interactions: 53782
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" O   HIS G  44 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   PRO A 332 "
            pdb=" OG1 THR A 335 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OD1 ASP B 205 "
            pdb=" OG  SER B 207 "
     model   vdw
     2.262 3.040
  ... (remaining 53777 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.700
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     5.720
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
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   0.052   6702  Z= 0.145
  Angle     :  0.495   6.961   9159  Z= 0.273
  Chirality :  0.040   0.154   1094
  Planarity :  0.003   0.047   1153
  Dihedral  : 12.286  69.718   2193
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.32 (0.28), residues: 876
  helix:  2.43 (0.25), residues: 385
  sheet:  0.27 (0.39), residues: 182
  loop : -0.76 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 356 
 TYR   0.029   0.001   TYR B  59 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.009   0.001   TRP R 158 
 HIS   0.002   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6701)
  covalent geometry    : angle       0.49459 ( 9157)
  SS BOND              : bond        0.00238 (    1)
  SS BOND              : angle       1.11675 (    2)
  hydrogen bonds       : bond        0.15337 (  383)
  hydrogen bonds       : angle       6.14233 ( 1122)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.218 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0737
  time to fit residues: 10.1984
Evaluate side-chains
  85 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0020
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.6388

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN
R 318 ASN
** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.126255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.108824 restraints weight = 10602.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 2.13
r_work: 0.3222 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3077 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.0817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6702  Z= 0.130
  Angle     :  0.479   5.612   9159  Z= 0.266
  Chirality :  0.041   0.139   1094
  Planarity :  0.004   0.046   1153
  Dihedral  :  4.011  18.763    964
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  9.35 %
    Favored  : 89.84 %
  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:  1.41 (0.28), residues: 876
  helix:  2.42 (0.26), residues: 396
  sheet:  0.41 (0.36), residues: 180
  loop : -0.76 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 251 
 TYR   0.024   0.001   TYR B  59 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.022   0.001   TRP B  82 
 HIS   0.002   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6701)
  covalent geometry    : angle       0.47920 ( 9157)
  SS BOND              : bond        0.00337 (    1)
  SS BOND              : angle       1.10766 (    2)
  hydrogen bonds       : bond        0.04404 (  383)
  hydrogen bonds       : angle       4.47005 ( 1122)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.248 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 99
  average time/residue: 0.0670
  time to fit residues: 9.3350
Evaluate side-chains
  95 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain R residue   87 VAL
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  205 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 58 optimal weight:    0.5980
   chunk 78 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 67 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 82 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
R 178 HIS
R 231 GLN
** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.125433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.107924 restraints weight = 10501.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.11
r_work: 0.3209 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.1139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6702  Z= 0.135
  Angle     :  0.464   5.813   9159  Z= 0.257
  Chirality :  0.041   0.134   1094
  Planarity :  0.003   0.048   1153
  Dihedral  :  4.012  21.493    964
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 11.77 %
    Favored  : 86.45 %
  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:  1.39 (0.28), residues: 876
  helix:  2.41 (0.25), residues: 397
  sheet:  0.41 (0.37), residues: 181
  loop : -0.82 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 356 
 TYR   0.022   0.001   TYR B  59 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.019   0.001   TRP B  82 
 HIS   0.002   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6701)
  covalent geometry    : angle       0.46382 ( 9157)
  SS BOND              : bond        0.00364 (    1)
  SS BOND              : angle       1.08645 (    2)
  hydrogen bonds       : bond        0.04081 (  383)
  hydrogen bonds       : angle       4.12079 ( 1122)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A  372 ILE cc_start: 0.8701 (mp) cc_final: 0.8363 (mt)
  outliers start: 11
  outliers final: 8
  residues processed: 104
  average time/residue: 0.0800
  time to fit residues: 11.2113
Evaluate side-chains
  96 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  205 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 78 optimal weight:    0.0980
   chunk 55 optimal weight:    2.9990
   chunk 74 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9980
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN
** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.126039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.108598 restraints weight = 10625.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 2.11
r_work: 0.3211 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6702  Z= 0.118
  Angle     :  0.447   5.693   9159  Z= 0.247
  Chirality :  0.040   0.131   1094
  Planarity :  0.003   0.048   1153
  Dihedral  :  3.935  22.895    964
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 12.42 %
    Favored  : 86.13 %
  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:  1.44 (0.28), residues: 876
  helix:  2.52 (0.26), residues: 396
  sheet:  0.50 (0.38), residues: 174
  loop : -0.90 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 251 
 TYR   0.017   0.001   TYR A 318 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.020   0.001   TRP B  82 
 HIS   0.002   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 6701)
  covalent geometry    : angle       0.44687 ( 9157)
  SS BOND              : bond        0.00297 (    1)
  SS BOND              : angle       0.95693 (    2)
  hydrogen bonds       : bond        0.03824 (  383)
  hydrogen bonds       : angle       3.98560 ( 1122)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  372 ILE cc_start: 0.8684 (mp) cc_final: 0.8361 (mt)
  outliers start: 9
  outliers final: 7
  residues processed: 100
  average time/residue: 0.0666
  time to fit residues: 9.2867
Evaluate side-chains
  92 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   87 VAL
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  196 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    0.0470
   chunk 54 optimal weight:    0.6980
   chunk 67 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.7282

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN
** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.124395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.107282 restraints weight = 10661.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 2.08
r_work: 0.3200 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3061 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6702  Z= 0.132
  Angle     :  0.458   6.482   9159  Z= 0.251
  Chirality :  0.041   0.132   1094
  Planarity :  0.003   0.048   1153
  Dihedral  :  3.968  24.228    964
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 13.06 %
    Favored  : 85.00 %
  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:  1.37 (0.28), residues: 876
  helix:  2.59 (0.26), residues: 390
  sheet:  0.29 (0.38), residues: 176
  loop : -0.95 (0.33), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 251 
 TYR   0.016   0.001   TYR B  59 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.019   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6701)
  covalent geometry    : angle       0.45739 ( 9157)
  SS BOND              : bond        0.00365 (    1)
  SS BOND              : angle       1.04899 (    2)
  hydrogen bonds       : bond        0.03868 (  383)
  hydrogen bonds       : angle       3.95319 ( 1122)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A  372 ILE cc_start: 0.8712 (mp) cc_final: 0.8380 (mt)
REVERT: B   59 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.8394 (m-80)
  outliers start: 12
  outliers final: 8
  residues processed: 98
  average time/residue: 0.0560
  time to fit residues: 8.0863
Evaluate side-chains
  94 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   87 VAL
Chi-restraints excluded: chain R residue  196 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 16 optimal weight:    0.4980
   chunk 84 optimal weight:    0.0470
   chunk 25 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0970
   chunk 21 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.3676

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN
** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.126830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.109767 restraints weight = 10695.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 2.09
r_work: 0.3233 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.1530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6702  Z= 0.097
  Angle     :  0.440  10.549   9159  Z= 0.238
  Chirality :  0.040   0.129   1094
  Planarity :  0.003   0.048   1153
  Dihedral  :  3.814  23.765    964
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 12.90 %
    Favored  : 84.35 %
  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:  1.48 (0.28), residues: 876
  helix:  2.60 (0.26), residues: 397
  sheet:  0.36 (0.38), residues: 174
  loop : -0.87 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 251 
 TYR   0.011   0.001   TYR A 318 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.019   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 6701)
  covalent geometry    : angle       0.43994 ( 9157)
  SS BOND              : bond        0.00155 (    1)
  SS BOND              : angle       0.74595 (    2)
  hydrogen bonds       : bond        0.03539 (  383)
  hydrogen bonds       : angle       3.82590 ( 1122)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A  372 ILE cc_start: 0.8713 (mp) cc_final: 0.8396 (mt)
REVERT: B   59 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.8325 (m-80)
REVERT: B  228 ASP cc_start: 0.8167 (m-30) cc_final: 0.7822 (m-30)
REVERT: R   65 GLN cc_start: 0.9240 (mt0) cc_final: 0.8776 (mp10)
  outliers start: 17
  outliers final: 13
  residues processed: 109
  average time/residue: 0.0616
  time to fit residues: 9.3461
Evaluate side-chains
  104 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   24 ASN
Chi-restraints excluded: chain R residue   87 VAL
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 4 optimal weight:    0.2980
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN
** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.123599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.106490 restraints weight = 10265.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.00
r_work: 0.3222 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.1629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6702  Z= 0.129
  Angle     :  0.481  13.671   9159  Z= 0.256
  Chirality :  0.041   0.159   1094
  Planarity :  0.003   0.048   1153
  Dihedral  :  3.917  25.011    964
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 13.71 %
    Favored  : 83.55 %
  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:  1.38 (0.28), residues: 876
  helix:  2.63 (0.26), residues: 391
  sheet:  0.12 (0.37), residues: 181
  loop : -0.89 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 251 
 TYR   0.015   0.001   TYR B  59 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6701)
  covalent geometry    : angle       0.48095 ( 9157)
  SS BOND              : bond        0.00327 (    1)
  SS BOND              : angle       0.89752 (    2)
  hydrogen bonds       : bond        0.03767 (  383)
  hydrogen bonds       : angle       3.86178 ( 1122)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A  372 ILE cc_start: 0.8754 (mp) cc_final: 0.8453 (mt)
REVERT: B   59 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.8332 (m-80)
REVERT: B  228 ASP cc_start: 0.8215 (m-30) cc_final: 0.7873 (m-30)
  outliers start: 17
  outliers final: 12
  residues processed: 103
  average time/residue: 0.0679
  time to fit residues: 9.6785
Evaluate side-chains
  102 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   24 ASN
Chi-restraints excluded: chain R residue   87 VAL
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0060
   chunk 63 optimal weight:    0.7980
   chunk 58 optimal weight:    0.7980
   chunk 79 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 87 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN
** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.124190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.107063 restraints weight = 10401.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 2.01
r_work: 0.3228 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3089 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6702  Z= 0.115
  Angle     :  0.470  13.378   9159  Z= 0.251
  Chirality :  0.041   0.189   1094
  Planarity :  0.003   0.047   1153
  Dihedral  :  3.906  24.930    964
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 13.71 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.28), residues: 876
  helix:  2.58 (0.26), residues: 391
  sheet:  0.15 (0.37), residues: 180
  loop : -0.92 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 251 
 TYR   0.013   0.001   TYR B  59 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6701)
  covalent geometry    : angle       0.47014 ( 9157)
  SS BOND              : bond        0.00258 (    1)
  SS BOND              : angle       0.78910 (    2)
  hydrogen bonds       : bond        0.03690 (  383)
  hydrogen bonds       : angle       3.84357 ( 1122)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A  372 ILE cc_start: 0.8761 (mp) cc_final: 0.8465 (mt)
REVERT: B   59 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.8336 (m-80)
REVERT: B  228 ASP cc_start: 0.8143 (m-30) cc_final: 0.7813 (m-30)
  outliers start: 19
  outliers final: 13
  residues processed: 102
  average time/residue: 0.0586
  time to fit residues: 8.3745
Evaluate side-chains
  101 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   87 VAL
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  314 ILE
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0870
   chunk 37 optimal weight:    0.1980
   chunk 45 optimal weight:    0.5980
   chunk 17 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 68 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN
** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.125048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.107927 restraints weight = 10309.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 2.01
r_work: 0.3240 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.1776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6702  Z= 0.108
  Angle     :  0.462  13.431   9159  Z= 0.247
  Chirality :  0.041   0.186   1094
  Planarity :  0.003   0.048   1153
  Dihedral  :  3.877  24.801    964
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 13.87 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.38 (0.29), residues: 876
  helix:  2.61 (0.26), residues: 391
  sheet:  0.13 (0.37), residues: 185
  loop : -0.89 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 251 
 TYR   0.012   0.001   TYR B  59 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 6701)
  covalent geometry    : angle       0.46148 ( 9157)
  SS BOND              : bond        0.00201 (    1)
  SS BOND              : angle       0.78575 (    2)
  hydrogen bonds       : bond        0.03593 (  383)
  hydrogen bonds       : angle       3.80157 ( 1122)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A  233 LYS cc_start: 0.7860 (mtpp) cc_final: 0.7528 (mtpp)
REVERT: A  372 ILE cc_start: 0.8757 (mp) cc_final: 0.8464 (mt)
REVERT: B   59 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.8320 (m-80)
REVERT: B  228 ASP cc_start: 0.8120 (m-30) cc_final: 0.7825 (m-30)
  outliers start: 18
  outliers final: 14
  residues processed: 105
  average time/residue: 0.0677
  time to fit residues: 9.8498
Evaluate side-chains
  104 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain R residue   87 VAL
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  314 ILE
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 59 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0570
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
B 293 ASN
R 231 GLN
** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.124171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.107082 restraints weight = 10284.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 2.00
r_work: 0.3229 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3090 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6702  Z= 0.121
  Angle     :  0.481  13.878   9159  Z= 0.255
  Chirality :  0.041   0.202   1094
  Planarity :  0.003   0.048   1153
  Dihedral  :  3.925  25.205    964
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 14.19 %
    Favored  : 83.06 %
  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:  1.37 (0.29), residues: 876
  helix:  2.59 (0.26), residues: 391
  sheet:  0.13 (0.37), residues: 185
  loop : -0.87 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 251 
 TYR   0.014   0.001   TYR B  59 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6701)
  covalent geometry    : angle       0.48083 ( 9157)
  SS BOND              : bond        0.00257 (    1)
  SS BOND              : angle       0.88140 (    2)
  hydrogen bonds       : bond        0.03694 (  383)
  hydrogen bonds       : angle       3.80813 ( 1122)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  233 LYS cc_start: 0.7781 (mtpp) cc_final: 0.7271 (mtpp)
REVERT: A  372 ILE cc_start: 0.8761 (mp) cc_final: 0.8468 (mt)
REVERT: B   59 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.8333 (m-80)
REVERT: B  228 ASP cc_start: 0.8151 (m-30) cc_final: 0.7806 (m-30)
  outliers start: 17
  outliers final: 14
  residues processed: 102
  average time/residue: 0.0766
  time to fit residues: 10.9268
Evaluate side-chains
  103 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain R residue   87 VAL
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  314 ILE
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 77 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 54 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 84 optimal weight:    0.8980
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.123626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.106548 restraints weight = 10322.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.00
r_work: 0.3222 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6702  Z= 0.135
  Angle     :  0.493  13.798   9159  Z= 0.263
  Chirality :  0.042   0.200   1094
  Planarity :  0.003   0.048   1153
  Dihedral  :  3.996  25.341    964
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 15.00 %
    Favored  : 82.74 %
  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:  1.30 (0.29), residues: 876
  helix:  2.51 (0.26), residues: 391
  sheet:  0.11 (0.37), residues: 185
  loop : -0.88 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 251 
 TYR   0.015   0.001   TYR B  59 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 6701)
  covalent geometry    : angle       0.49239 ( 9157)
  SS BOND              : bond        0.00312 (    1)
  SS BOND              : angle       0.94906 (    2)
  hydrogen bonds       : bond        0.03791 (  383)
  hydrogen bonds       : angle       3.83286 ( 1122)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1491.96 seconds
wall clock time: 26 minutes 16.71 seconds (1576.71 seconds total)