Starting phenix.real_space_refine
on Wed Sep 17 07:18:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9g3f_50997/09_2025/9g3f_50997.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g3f_50997/09_2025/9g3f_50997.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g3f_50997/09_2025/9g3f_50997.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g3f_50997/09_2025/9g3f_50997.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9g3f_50997/09_2025/9g3f_50997.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g3f_50997/09_2025/9g3f_50997.map"
  }
  resolution = 3.36
  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=   0.007 sd=   0.107
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      20      5.16       5
     C    4317      2.51       5
     N    1015      2.21       5
     O    1065      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6419
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 393, 3200
          Classifications: {'peptide': 393}
          Link IDs: {'PTRANS': 14, 'TRANS': 378}
    Chain: "B"
      Number of atoms: 3128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 385, 3128
          Classifications: {'peptide': 385}
          Link IDs: {'PTRANS': 14, 'TRANS': 370}
    Chain: "A"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 46
          Unusual residues: {'PGT': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 5
    Chain: "B"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 45
          Unusual residues: {'PGT': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 6
  Time building chain proxies: 1.85, per 1000 atoms: 0.29
  Number of scatterers: 6419
  At special positions: 0
  Unit cell: (62.342, 105.266, 99.134, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      20     16.00
     P       2     15.00
     O    1065      8.00
     N    1015      7.00
     C    4317      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: 0.53
  Conformation dependent library (CDL) restraints added in 384.2 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1456

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 2 sheets defined
      85.7% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 29
      removed outlier: 4.680A  pdb=" N   PHE A  17 " --> pdb=" O   PHE A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 38
    Processing helix  chain 'A' and resid 48 through 53
      removed outlier: 3.620A  pdb=" N   PHE A  52 " --> pdb=" O   ALA A  49 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   TRP A  53 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 78
      removed outlier: 3.815A  pdb=" N   ILE A  59 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   PHE A  60 " --> pdb=" O   ASP A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 88
    Processing helix  chain 'A' and resid 88 through 125
      removed outlier: 3.507A  pdb=" N   VAL A 102 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ALA A 113 " --> pdb=" O   ASN A 109 " (cutoff:3.500A)
      Proline residue:  A 114  - end of helix
      removed outlier: 3.804A  pdb=" N   SER A 125 " --> pdb=" O   THR A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 175
      removed outlier: 3.517A  pdb=" N   PHE A 134 " --> pdb=" O   THR A 130 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   GLU A 137 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   PHE A 141 " --> pdb=" O   GLU A 137 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   LEU A 154 " --> pdb=" O   VAL A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 182
    Processing helix  chain 'A' and resid 186 through 193
    Processing helix  chain 'A' and resid 193 through 227
      removed outlier: 3.878A  pdb=" N   ALA A 199 " --> pdb=" O   THR A 195 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ASN A 204 " --> pdb=" O   SER A 200 " (cutoff:3.500A)
      Proline residue:  A 221  - end of helix
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 241 through 253
    Processing helix  chain 'A' and resid 256 through 262
    Processing helix  chain 'A' and resid 263 through 289
      removed outlier: 4.378A  pdb=" N   GLY A 267 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LYS A 271 " --> pdb=" O   GLY A 267 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ASN A 272 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ASP A 288 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 337
      removed outlier: 4.381A  pdb=" N   VAL A 298 " --> pdb=" O   THR A 294 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ARG A 299 " --> pdb=" O   PRO A 295 " (cutoff:3.500A)
      removed outlier: 5.304A  pdb=" N   GLU A 300 " --> pdb=" O   PRO A 296 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   ARG A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   TYR A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   PHE A 319 " --> pdb=" O   HIS A 315 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   VAL A 332 " --> pdb=" O   GLN A 328 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   GLY A 334 " --> pdb=" O   ASP A 330 " (cutoff:3.500A)
      removed outlier: 5.350A  pdb=" N   LEU A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 344
      removed outlier: 3.544A  pdb=" N   ALA A 344 " --> pdb=" O   PRO A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 390
      removed outlier: 4.412A  pdb=" N   ARG A 385 " --> pdb=" O   SER A 381 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   GLU A 390 " --> pdb=" O   LEU A 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 29
    Processing helix  chain 'B' and resid 32 through 40
    Processing helix  chain 'B' and resid 48 through 53
      removed outlier: 3.557A  pdb=" N   ARG B  51 " --> pdb=" O   SER B  48 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   PHE B  52 " --> pdb=" O   ALA B  49 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   TRP B  53 " --> pdb=" O   ALA B  50 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 48 through 53'
    Processing helix  chain 'B' and resid 54 through 76
      removed outlier: 3.833A  pdb=" N   PHE B  60 " --> pdb=" O   ASP B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 88
    Processing helix  chain 'B' and resid 88 through 125
      removed outlier: 3.608A  pdb=" N   VAL B 102 " --> pdb=" O   THR B  98 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   GLY B 105 " --> pdb=" O   LEU B 101 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   ALA B 113 " --> pdb=" O   ASN B 109 " (cutoff:3.500A)
      Proline residue:  B 114  - end of helix
      removed outlier: 3.712A  pdb=" N   SER B 125 " --> pdb=" O   THR B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 177
      removed outlier: 3.733A  pdb=" N   PHE B 134 " --> pdb=" O   THR B 130 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ARG B 136 " --> pdb=" O   GLU B 132 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLU B 137 " --> pdb=" O   GLN B 133 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL B 140 " --> pdb=" O   ARG B 136 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLY B 143 " --> pdb=" O   GLY B 139 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   HIS B 161 " --> pdb=" O   PHE B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 182
    Processing helix  chain 'B' and resid 193 through 227
      removed outlier: 3.528A  pdb=" N   ARG B 197 " --> pdb=" O   GLU B 193 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   THR B 201 " --> pdb=" O   ARG B 197 " (cutoff:3.500A)
      Proline residue:  B 221  - end of helix
    Processing helix  chain 'B' and resid 228 through 230
      No H-bonds generated for 'chain 'B' and resid 228 through 230'
    Processing helix  chain 'B' and resid 241 through 254
      removed outlier: 3.687A  pdb=" N   GLY B 254 " --> pdb=" O   TRP B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 262
      removed outlier: 3.608A  pdb=" N   GLY B 262 " --> pdb=" O   LEU B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 289
      removed outlier: 4.480A  pdb=" N   GLY B 267 " --> pdb=" O   ILE B 263 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ASP B 288 " --> pdb=" O   VAL B 284 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ASP B 289 " --> pdb=" O   TYR B 285 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 337
      removed outlier: 3.761A  pdb=" N   GLU B 300 " --> pdb=" O   PRO B 296 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LYS B 307 " --> pdb=" O   SER B 303 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ASN B 308 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   TYR B 318 " --> pdb=" O   PHE B 314 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   VAL B 332 " --> pdb=" O   GLN B 328 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   GLY B 334 " --> pdb=" O   ASP B 330 " (cutoff:3.500A)
      removed outlier: 5.358A  pdb=" N   LEU B 335 " --> pdb=" O   ASN B 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 344
      removed outlier: 3.621A  pdb=" N   ALA B 344 " --> pdb=" O   PRO B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 371
      removed outlier: 3.534A  pdb=" N   GLY B 360 " --> pdb=" O   THR B 356 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   TYR B 368 " --> pdb=" O   GLY B 364 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   LEU B 369 " --> pdb=" O   ALA B 365 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ILE B 370 " --> pdb=" O   PHE B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 384
      removed outlier: 4.038A  pdb=" N   MET B 380 " --> pdb=" O   LEU B 376 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 232 through 233
      removed outlier: 3.533A  pdb=" N   GLY A 237 " --> pdb=" O   LEU A 233 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 232 through 233

    462 hydrogen bonds defined for protein.
    1380 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.01

  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:
        1.20 -     1.32: 991
        1.32 -     1.44: 2016
        1.44 -     1.56: 3572
        1.56 -     1.68: 4
        1.68 -     1.80: 38
  Bond restraints: 6621
  Sorted by residual:
  bond pdb=" C   VAL B 191 "
       pdb=" O   VAL B 191 "
    ideal  model  delta    sigma   weight residual
    1.242  1.226  0.016 1.23e-02 6.61e+03 1.73e+00
  bond pdb=" C   PRO A 295 "
       pdb=" N   PRO A 296 "
    ideal  model  delta    sigma   weight residual
    1.334  1.359 -0.025 2.34e-02 1.83e+03 1.14e+00
  bond pdb=" N   ILE A  45 "
       pdb=" CA  ILE A  45 "
    ideal  model  delta    sigma   weight residual
    1.454  1.462 -0.007 7.70e-03 1.69e+04 9.15e-01
  bond pdb=" CA  HIS B  81 "
       pdb=" C   HIS B  81 "
    ideal  model  delta    sigma   weight residual
    1.520  1.531 -0.011 1.37e-02 5.33e+03 6.37e-01
  bond pdb=" CA  VAL B 191 "
       pdb=" C   VAL B 191 "
    ideal  model  delta    sigma   weight residual
    1.520  1.531 -0.012 1.47e-02 4.63e+03 6.32e-01
  ... (remaining 6616 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 8807
        1.51 -     3.01: 167
        3.01 -     4.52: 30
        4.52 -     6.03: 11
        6.03 -     7.54: 1
  Bond angle restraints: 9016
  Sorted by residual:
  angle pdb=" CA  ARG B  82 "
        pdb=" CB  ARG B  82 "
        pdb=" CG  ARG B  82 "
      ideal   model   delta    sigma   weight residual
     114.10  119.33   -5.23 2.00e+00 2.50e-01 6.84e+00
  angle pdb=" N   ALA A  29 "
        pdb=" CA  ALA A  29 "
        pdb=" C   ALA A  29 "
      ideal   model   delta    sigma   weight residual
     110.44  107.41    3.03 1.20e+00 6.94e-01 6.36e+00
  angle pdb=" N   LEU B 369 "
        pdb=" CA  LEU B 369 "
        pdb=" C   LEU B 369 "
      ideal   model   delta    sigma   weight residual
     112.93  109.72    3.21 1.33e+00 5.65e-01 5.82e+00
  angle pdb=" N   GLN B 189 "
        pdb=" CA  GLN B 189 "
        pdb=" C   GLN B 189 "
      ideal   model   delta    sigma   weight residual
     114.75  111.72    3.03 1.26e+00 6.30e-01 5.77e+00
  angle pdb=" N   VAL B 191 "
        pdb=" CA  VAL B 191 "
        pdb=" C   VAL B 191 "
      ideal   model   delta    sigma   weight residual
     113.43  110.92    2.51 1.09e+00 8.42e-01 5.28e+00
  ... (remaining 9011 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.25: 3624
       28.25 -    56.50: 124
       56.50 -    84.75: 10
       84.75 -   113.00: 2
      113.00 -   141.24: 1
  Dihedral angle restraints: 3761
    sinusoidal: 1487
      harmonic: 2274
  Sorted by residual:
  dihedral pdb=" C3  PGT A 501 "
           pdb=" C1  PGT A 501 "
           pdb=" C2  PGT A 501 "
           pdb=" O3P PGT A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     293.87  152.63  141.24     1      3.00e+01 1.11e-03 1.90e+01
  dihedral pdb=" C3  PGT B 501 "
           pdb=" C1  PGT B 501 "
           pdb=" C2  PGT B 501 "
           pdb=" O3P PGT B 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -66.13 -172.07  105.94     1      3.00e+01 1.11e-03 1.36e+01
  dihedral pdb=" CA  ALA B 188 "
           pdb=" C   ALA B 188 "
           pdb=" N   GLN B 189 "
           pdb=" CA  GLN B 189 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.48   16.52     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 3758 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 575
       0.027 -    0.054: 281
       0.054 -    0.081: 99
       0.081 -    0.109: 33
       0.109 -    0.136: 9
  Chirality restraints: 997
  Sorted by residual:
  chirality pdb=" CA  VAL A 129 "
            pdb=" N   VAL A 129 "
            pdb=" C   VAL A 129 "
            pdb=" CB  VAL A 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.61e-01
  chirality pdb=" CA  PRO A 234 "
            pdb=" N   PRO A 234 "
            pdb=" C   PRO A 234 "
            pdb=" CB  PRO A 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.12 2.00e-01 2.50e+01 3.85e-01
  chirality pdb=" CA  ILE B 239 "
            pdb=" N   ILE B 239 "
            pdb=" C   ILE B 239 "
            pdb=" CB  ILE B 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.50e-01
  ... (remaining 994 not shown)

  Planarity restraints: 1096
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 295 "    0.031 5.00e-02 4.00e+02   4.63e-02 3.42e+00
        pdb=" N   PRO B 296 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO B 296 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 296 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 295 "   -0.029 5.00e-02 4.00e+02   4.30e-02 2.96e+00
        pdb=" N   PRO A 296 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 296 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 296 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B  82 "   -0.008 2.00e-02 2.50e+03   1.50e-02 2.26e+00
        pdb=" C   ARG B  82 "    0.026 2.00e-02 2.50e+03
        pdb=" O   ARG B  82 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   TRP B  83 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1093 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1531
        2.78 -     3.31: 6372
        3.31 -     3.84: 10278
        3.84 -     4.37: 12336
        4.37 -     4.90: 20993
  Nonbonded interactions: 51510
  Sorted by model distance:
  nonbonded pdb=" O4P PGT A 501 "
            pdb=" O6  PGT A 501 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   ILE A  38 "
            pdb=" OG1 THR A  39 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OG1 THR A  91 "
            pdb=" OH  TYR A 162 "
     model   vdw
     2.355 3.040
  nonbonded pdb=" O   ARG B 197 "
            pdb=" OG1 THR B 201 "
     model   vdw
     2.357 3.040
  nonbonded pdb=" OE1 GLN A 179 "
            pdb=" NH2 ARG A 182 "
     model   vdw
     2.361 3.120
  ... (remaining 51505 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' and (resid 2 through 386 or (resid 501 and (name C1 or name C11 or na \ 
me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ 
r name C19 or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 \ 
 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ 
 C38 or name C39 or name C4 or name C40 or name C41 or name C42 or name C43 or n \ 
ame C44 or name C45 or name C46 or name C5 or name C6 or name O11 or name O1P or \ 
 name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name O5 o \ 
r name O6 or name P ))))
  selection = chain 'B'
}

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 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:             1.680
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.410
  Find NCS groups from input model:        0.110
  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:             0.000
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
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   0.025   6621  Z= 0.125
  Angle     :  0.541   7.537   9016  Z= 0.313
  Chirality :  0.037   0.136    997
  Planarity :  0.004   0.046   1096
  Dihedral  : 14.154 141.244   2305
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  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: -1.83 (0.28), residues: 774
  helix: -0.92 (0.19), residues: 626
  sheet:  None (None), residues: 0
  loop : -1.71 (0.48), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 292 
 TYR   0.015   0.001   TYR A  78 
 PHE   0.019   0.001   PHE A  57 
 TRP   0.009   0.001   TRP A  53 
 HIS   0.008   0.001   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 6621)
  covalent geometry    : angle       0.54105 ( 9016)
  hydrogen bonds       : bond        0.25070 (  462)
  hydrogen bonds       : angle       8.14182 ( 1380)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A  318 TYR cc_start: 0.7813 (m-10) cc_final: 0.6944 (m-10)
REVERT: A  352 MET cc_start: 0.8638 (ttp) cc_final: 0.8310 (ttt)
REVERT: B  318 TYR cc_start: 0.7908 (m-10) cc_final: 0.6903 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.0792
  time to fit residues: 7.9061
Evaluate side-chains
  68 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.145845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.113600 restraints weight = 7813.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 1.92
r_work: 0.3137 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6621  Z= 0.153
  Angle     :  0.573   8.115   9016  Z= 0.310
  Chirality :  0.040   0.129    997
  Planarity :  0.004   0.043   1096
  Dihedral  :  9.487 138.210    940
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  6.25 %
    Favored  : 93.29 %
  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: -0.24 (0.29), residues: 774
  helix:  0.29 (0.20), residues: 635
  sheet:  None (None), residues: 0
  loop : -1.82 (0.50), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 197 
 TYR   0.011   0.001   TYR B 162 
 PHE   0.017   0.002   PHE A 164 
 TRP   0.013   0.001   TRP A  34 
 HIS   0.007   0.001   HIS A 391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 6621)
  covalent geometry    : angle       0.57259 ( 9016)
  hydrogen bonds       : bond        0.06012 (  462)
  hydrogen bonds       : angle       4.66394 ( 1380)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 0.233 
Fit side-chains
REVERT: A   13 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.6128 (m-80)
REVERT: A  330 ASP cc_start: 0.8575 (t0) cc_final: 0.8214 (t0)
REVERT: B  330 ASP cc_start: 0.8566 (t0) cc_final: 0.8216 (t0)
REVERT: B  346 THR cc_start: 0.8900 (m) cc_final: 0.8664 (p)
  outliers start: 3
  outliers final: 1
  residues processed: 73
  average time/residue: 0.0855
  time to fit residues: 8.4843
Evaluate side-chains
  68 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 66
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain B residue  257 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 3 optimal weight:    0.0970
   chunk 20 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.146636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.115568 restraints weight = 7701.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 1.83
r_work: 0.3154 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6621  Z= 0.139
  Angle     :  0.525   7.298   9016  Z= 0.282
  Chirality :  0.040   0.129    997
  Planarity :  0.004   0.042   1096
  Dihedral  :  9.085 137.124    940
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  7.77 %
    Favored  : 91.31 %
  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:  0.28 (0.30), residues: 774
  helix:  0.66 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -1.73 (0.54), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 197 
 TYR   0.012   0.001   TYR B 162 
 PHE   0.015   0.001   PHE A 164 
 TRP   0.011   0.001   TRP A  34 
 HIS   0.007   0.001   HIS A 391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6621)
  covalent geometry    : angle       0.52492 ( 9016)
  hydrogen bonds       : bond        0.05129 (  462)
  hydrogen bonds       : angle       4.23743 ( 1380)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A   13 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.6219 (m-80)
REVERT: A   56 ASP cc_start: 0.8788 (t0) cc_final: 0.8184 (t0)
REVERT: A  128 LYS cc_start: 0.8772 (ttpt) cc_final: 0.8530 (ttmm)
REVERT: A  390 GLU cc_start: 0.6715 (tm-30) cc_final: 0.6467 (tm-30)
REVERT: B  282 GLU cc_start: 0.7233 (tp30) cc_final: 0.6620 (tp30)
REVERT: B  330 ASP cc_start: 0.8507 (t0) cc_final: 0.8240 (t0)
  outliers start: 6
  outliers final: 1
  residues processed: 71
  average time/residue: 0.0825
  time to fit residues: 7.9076
Evaluate side-chains
  67 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain B residue  257 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 30 optimal weight:    0.0770
   chunk 16 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 72 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.146338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.114172 restraints weight = 7904.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 1.94
r_work: 0.3159 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6621  Z= 0.133
  Angle     :  0.513  10.270   9016  Z= 0.272
  Chirality :  0.039   0.128    997
  Planarity :  0.004   0.042   1096
  Dihedral  :  8.699 137.576    940
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  9.91 %
    Favored  : 89.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.30), residues: 774
  helix:  0.85 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -1.73 (0.54), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 197 
 TYR   0.015   0.001   TYR A 316 
 PHE   0.015   0.001   PHE A 164 
 TRP   0.010   0.001   TRP A  34 
 HIS   0.007   0.001   HIS A 391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6621)
  covalent geometry    : angle       0.51325 ( 9016)
  hydrogen bonds       : bond        0.04677 (  462)
  hydrogen bonds       : angle       4.03500 ( 1380)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A   13 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.6512 (m-80)
REVERT: A   56 ASP cc_start: 0.8909 (t0) cc_final: 0.8246 (t0)
REVERT: A  128 LYS cc_start: 0.8908 (ttpt) cc_final: 0.8581 (ttmm)
  outliers start: 6
  outliers final: 5
  residues processed: 71
  average time/residue: 0.0761
  time to fit residues: 7.6451
Evaluate side-chains
  72 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain B residue  257 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 74 optimal weight:    0.6980
   chunk 49 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9990
   chunk 26 optimal weight:    0.3980
   chunk 1 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 315 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.146484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.114535 restraints weight = 7879.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 1.93
r_work: 0.3163 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6621  Z= 0.131
  Angle     :  0.506   7.980   9016  Z= 0.269
  Chirality :  0.039   0.128    997
  Planarity :  0.004   0.043   1096
  Dihedral  :  8.429 138.062    940
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  9.30 %
    Favored  : 89.33 %
  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:  0.70 (0.30), residues: 774
  helix:  0.97 (0.20), residues: 639
  sheet:  None (None), residues: 0
  loop : -1.76 (0.55), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 197 
 TYR   0.012   0.001   TYR B 162 
 PHE   0.014   0.001   PHE A 164 
 TRP   0.011   0.001   TRP A  34 
 HIS   0.007   0.001   HIS A 391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6621)
  covalent geometry    : angle       0.50594 ( 9016)
  hydrogen bonds       : bond        0.04569 (  462)
  hydrogen bonds       : angle       3.96620 ( 1380)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A   13 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.6714 (m-80)
REVERT: A   56 ASP cc_start: 0.8898 (t0) cc_final: 0.8194 (t0)
REVERT: A   78 TYR cc_start: 0.7475 (t80) cc_final: 0.7243 (t80)
REVERT: A  128 LYS cc_start: 0.8918 (ttpt) cc_final: 0.8542 (ttmm)
REVERT: A  252 LEU cc_start: 0.6307 (OUTLIER) cc_final: 0.6044 (tt)
REVERT: A  316 TYR cc_start: 0.7713 (t80) cc_final: 0.7238 (t80)
REVERT: B   34 TRP cc_start: 0.7227 (t-100) cc_final: 0.7006 (t-100)
  outliers start: 9
  outliers final: 6
  residues processed: 74
  average time/residue: 0.0763
  time to fit residues: 8.0159
Evaluate side-chains
  72 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  294 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0970
   chunk 29 optimal weight:    0.0770
   chunk 42 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.5936

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

Flipped N/Q/H residues before XYZ refinement:
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.146677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.114676 restraints weight = 7970.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 1.94
r_work: 0.3165 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3019 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6621  Z= 0.127
  Angle     :  0.507   7.322   9016  Z= 0.271
  Chirality :  0.038   0.127    997
  Planarity :  0.004   0.051   1096
  Dihedral  :  8.297 138.248    940
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 10.06 %
    Favored  : 88.57 %
  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:  0.80 (0.30), residues: 774
  helix:  1.06 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -1.79 (0.53), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 197 
 TYR   0.011   0.001   TYR B 162 
 PHE   0.013   0.001   PHE A 164 
 TRP   0.011   0.001   TRP A  34 
 HIS   0.006   0.001   HIS A 391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6621)
  covalent geometry    : angle       0.50688 ( 9016)
  hydrogen bonds       : bond        0.04459 (  462)
  hydrogen bonds       : angle       3.93059 ( 1380)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A   13 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.6676 (m-80)
REVERT: A   56 ASP cc_start: 0.8939 (t0) cc_final: 0.8225 (t0)
REVERT: A   78 TYR cc_start: 0.7510 (t80) cc_final: 0.7282 (t80)
REVERT: A  252 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6143 (tt)
REVERT: A  316 TYR cc_start: 0.7758 (t80) cc_final: 0.7261 (t80)
  outliers start: 9
  outliers final: 7
  residues processed: 71
  average time/residue: 0.0761
  time to fit residues: 7.6763
Evaluate side-chains
  73 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  112 TYR
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  294 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 38 optimal weight:    0.3980
   chunk 1 optimal weight:    0.8980
   chunk 75 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0050
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.146855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.115020 restraints weight = 7911.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 1.93
r_work: 0.3174 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3031 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.2654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6621  Z= 0.125
  Angle     :  0.498   6.093   9016  Z= 0.267
  Chirality :  0.038   0.127    997
  Planarity :  0.004   0.046   1096
  Dihedral  :  8.118 137.504    940
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  :  9.45 %
    Favored  : 88.72 %
  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:  0.97 (0.30), residues: 774
  helix:  1.16 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -1.59 (0.54), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 167 
 TYR   0.011   0.001   TYR B 162 
 PHE   0.014   0.001   PHE A 164 
 TRP   0.010   0.001   TRP A  34 
 HIS   0.006   0.001   HIS A 391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6621)
  covalent geometry    : angle       0.49800 ( 9016)
  hydrogen bonds       : bond        0.04384 (  462)
  hydrogen bonds       : angle       3.85478 ( 1380)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A   13 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.6728 (m-80)
REVERT: A   56 ASP cc_start: 0.8917 (t0) cc_final: 0.8257 (t0)
REVERT: A   78 TYR cc_start: 0.7483 (t80) cc_final: 0.7240 (t80)
REVERT: A  128 LYS cc_start: 0.8901 (ttpt) cc_final: 0.8525 (ttmm)
REVERT: A  131 ILE cc_start: 0.6883 (OUTLIER) cc_final: 0.6422 (mp)
REVERT: A  252 LEU cc_start: 0.6392 (OUTLIER) cc_final: 0.6130 (tt)
  outliers start: 12
  outliers final: 7
  residues processed: 81
  average time/residue: 0.0677
  time to fit residues: 7.8166
Evaluate side-chains
  77 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  294 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 4 optimal weight:    0.0970
   chunk 27 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 55 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0870
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.147692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.115901 restraints weight = 7857.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 1.92
r_work: 0.3188 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6621  Z= 0.120
  Angle     :  0.512  13.171   9016  Z= 0.268
  Chirality :  0.038   0.125    997
  Planarity :  0.004   0.059   1096
  Dihedral  :  8.019 136.755    940
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.71 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  :  9.76 %
    Favored  : 88.26 %
  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:  1.06 (0.30), residues: 774
  helix:  1.21 (0.20), residues: 635
  sheet:  None (None), residues: 0
  loop : -1.46 (0.54), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 167 
 TYR   0.016   0.001   TYR A 316 
 PHE   0.013   0.001   PHE A 164 
 TRP   0.010   0.001   TRP B  34 
 HIS   0.006   0.001   HIS A 391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6621)
  covalent geometry    : angle       0.51234 ( 9016)
  hydrogen bonds       : bond        0.04273 (  462)
  hydrogen bonds       : angle       3.82320 ( 1380)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A   13 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.6714 (m-80)
REVERT: A   56 ASP cc_start: 0.8956 (t0) cc_final: 0.8274 (t0)
REVERT: A   78 TYR cc_start: 0.7494 (t80) cc_final: 0.7251 (t80)
REVERT: A  131 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.6403 (mp)
  outliers start: 13
  outliers final: 8
  residues processed: 71
  average time/residue: 0.0722
  time to fit residues: 7.2460
Evaluate side-chains
  71 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  112 TYR
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  294 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 54 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 76 optimal weight:    4.9990
   chunk 74 optimal weight:    0.5980
   chunk 67 optimal weight:    0.5980
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.146234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.114281 restraints weight = 7956.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 1.93
r_work: 0.3160 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6621  Z= 0.133
  Angle     :  0.523  10.709   9016  Z= 0.274
  Chirality :  0.039   0.135    997
  Planarity :  0.004   0.051   1096
  Dihedral  :  8.018 134.961    940
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.84 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  :  9.60 %
    Favored  : 88.57 %
  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:  1.04 (0.30), residues: 774
  helix:  1.18 (0.20), residues: 633
  sheet:  None (None), residues: 0
  loop : -1.39 (0.55), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 167 
 TYR   0.013   0.001   TYR B 162 
 PHE   0.014   0.001   PHE A 164 
 TRP   0.009   0.001   TRP B  34 
 HIS   0.006   0.001   HIS A 391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6621)
  covalent geometry    : angle       0.52287 ( 9016)
  hydrogen bonds       : bond        0.04462 (  462)
  hydrogen bonds       : angle       3.86780 ( 1380)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A   13 PHE cc_start: 0.7564 (OUTLIER) cc_final: 0.6669 (m-80)
REVERT: A   56 ASP cc_start: 0.9044 (t0) cc_final: 0.8362 (t0)
REVERT: A   78 TYR cc_start: 0.7468 (t80) cc_final: 0.7245 (t80)
REVERT: A  131 ILE cc_start: 0.6922 (OUTLIER) cc_final: 0.6453 (mp)
  outliers start: 12
  outliers final: 8
  residues processed: 73
  average time/residue: 0.0679
  time to fit residues: 6.9757
Evaluate side-chains
  74 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  112 TYR
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  294 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 52 optimal weight:    0.2980
   chunk 40 optimal weight:    2.9990
   chunk 76 optimal weight:    8.9990
   chunk 37 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0570
   chunk 0 optimal weight:    3.9990
   chunk 63 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 273 GLN ** 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 = 0.3683 r_free = 0.3683 target = 0.148547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.126262 restraints weight = 7717.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 1.28
r_work: 0.3113 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6621  Z= 0.117
  Angle     :  0.501   9.646   9016  Z= 0.264
  Chirality :  0.038   0.124    997
  Planarity :  0.004   0.047   1096
  Dihedral  :  7.823 133.664    940
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.84 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  :  9.76 %
    Favored  : 88.41 %
  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:  1.17 (0.30), residues: 774
  helix:  1.28 (0.20), residues: 634
  sheet:  None (None), residues: 0
  loop : -1.41 (0.54), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 167 
 TYR   0.014   0.001   TYR A 316 
 PHE   0.013   0.001   PHE A 164 
 TRP   0.009   0.001   TRP A  34 
 HIS   0.006   0.001   HIS A 391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 6621)
  covalent geometry    : angle       0.50111 ( 9016)
  hydrogen bonds       : bond        0.04179 (  462)
  hydrogen bonds       : angle       3.76450 ( 1380)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A   13 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.6970 (m-80)
REVERT: A   56 ASP cc_start: 0.8971 (t0) cc_final: 0.8365 (t0)
REVERT: A   78 TYR cc_start: 0.7726 (t80) cc_final: 0.7482 (t80)
REVERT: A  131 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6631 (mp)
  outliers start: 12
  outliers final: 9
  residues processed: 69
  average time/residue: 0.0650
  time to fit residues: 6.5215
Evaluate side-chains
  72 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  112 TYR
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain B residue  170 MET
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  294 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0370
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 273 GLN ** 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 = 0.3672 r_free = 0.3672 target = 0.147565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.124289 restraints weight = 7694.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 1.32
r_work: 0.3085 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2950 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.2855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6621  Z= 0.126
  Angle     :  0.510   8.805   9016  Z= 0.269
  Chirality :  0.038   0.124    997
  Planarity :  0.004   0.045   1096
  Dihedral  :  7.820 132.230    940
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.71 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  :  9.91 %
    Favored  : 88.41 %
  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:  1.15 (0.30), residues: 774
  helix:  1.26 (0.20), residues: 634
  sheet:  None (None), residues: 0
  loop : -1.39 (0.54), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 167 
 TYR   0.012   0.001   TYR B 162 
 PHE   0.014   0.001   PHE A 164 
 TRP   0.009   0.001   TRP A  34 
 HIS   0.006   0.001   HIS A 391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6621)
  covalent geometry    : angle       0.50956 ( 9016)
  hydrogen bonds       : bond        0.04309 (  462)
  hydrogen bonds       : angle       3.79665 ( 1380)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1567.91 seconds
wall clock time: 27 minutes 33.83 seconds (1653.83 seconds total)