Starting phenix.real_space_refine
on Wed Sep 17 08:34:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hpg_52329/09_2025/9hpg_52329.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hpg_52329/09_2025/9hpg_52329.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.35
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hpg_52329/09_2025/9hpg_52329.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hpg_52329/09_2025/9hpg_52329.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hpg_52329/09_2025/9hpg_52329.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hpg_52329/09_2025/9hpg_52329.map"
  }
  resolution = 3.35
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
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      35      5.16       5
     C    4451      2.51       5
     N    1188      2.21       5
     O    1273      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 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: 6947
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 3002
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 3002
          Classifications: {'peptide': 375}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 11, 'TRANS': 363}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 40
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "C"
      Number of atoms: 3945
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 499, 3945
          Classifications: {'peptide': 499}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 481}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 65
          Unresolved non-hydrogen angles: 79
          Unresolved non-hydrogen dihedrals: 51
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 58
  Time building chain proxies: 1.80, per 1000 atoms: 0.26
  Number of scatterers: 6947
  At special positions: 0
  Unit cell: (84.995, 102.185, 109.825, 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      35     16.00
     O    1273      8.00
     N    1188      7.00
     C    4451      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  63 " - pdb=" SG  CYS B 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  63 " - pdb=" SG  CYS C 312 " 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: 0.52
  Conformation dependent library (CDL) restraints added in 352.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1640

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 8 sheets defined
      42.7% alpha, 13.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'B' and resid 17 through 32
    Processing helix  chain 'B' and resid 55 through 69
      removed outlier: 3.903A  pdb=" N   THR B  59 " --> pdb=" O   SER B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 80
      No H-bonds generated for 'chain 'B' and resid 78 through 80'
    Processing helix  chain 'B' and resid 81 through 93
      removed outlier: 3.690A  pdb=" N   LEU B  85 " --> pdb=" O   SER B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 128
    Processing helix  chain 'B' and resid 143 through 157
    Processing helix  chain 'B' and resid 170 through 184
      removed outlier: 4.032A  pdb=" N   PHE B 174 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ARG B 184 " --> pdb=" O   GLU B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 209
    Processing helix  chain 'B' and resid 229 through 236
      removed outlier: 3.679A  pdb=" N   GLY B 236 " --> pdb=" O   VAL B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 260
    Processing helix  chain 'B' and resid 276 through 299
      removed outlier: 3.679A  pdb=" N   ALA B 280 " --> pdb=" O   LYS B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 330
    Processing helix  chain 'C' and resid 16 through 33
    Processing helix  chain 'C' and resid 54 through 69
      removed outlier: 3.541A  pdb=" N   VAL C  58 " --> pdb=" O   ASN C  54 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 93
      removed outlier: 4.717A  pdb=" N   ASN C  83 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 5.200A  pdb=" N   THR C  84 " --> pdb=" O   MET C  80 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU C  85 " --> pdb=" O   SER C  81 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 129
    Processing helix  chain 'C' and resid 143 through 157
      removed outlier: 3.689A  pdb=" N   GLU C 151 " --> pdb=" O   GLN C 147 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   VAL C 154 " --> pdb=" O   MET C 150 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLN C 155 " --> pdb=" O   GLU C 151 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 170 through 184
      removed outlier: 3.959A  pdb=" N   PHE C 174 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ARG C 184 " --> pdb=" O   GLU C 180 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 194 through 209
      removed outlier: 3.770A  pdb=" N   VAL C 206 " --> pdb=" O   LEU C 202 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 224 through 227
      removed outlier: 3.893A  pdb=" N   ILE C 227 " --> pdb=" O   PHE C 224 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 224 through 227'
    Processing helix  chain 'C' and resid 229 through 236
      removed outlier: 3.886A  pdb=" N   HIS C 234 " --> pdb=" O   GLU C 230 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   GLY C 235 " --> pdb=" O   ARG C 231 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   GLY C 236 " --> pdb=" O   VAL C 232 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 249 through 260
    Processing helix  chain 'C' and resid 276 through 299
      removed outlier: 3.503A  pdb=" N   ALA C 280 " --> pdb=" O   LYS C 276 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ILE C 286 " --> pdb=" O   THR C 282 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU C 287 " --> pdb=" O   HIS C 283 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 322 through 331
    Processing helix  chain 'C' and resid 419 through 421
      No H-bonds generated for 'chain 'C' and resid 419 through 421'
    Processing helix  chain 'C' and resid 425 through 439
    Processing helix  chain 'C' and resid 463 through 471
    Processing helix  chain 'C' and resid 484 through 489
    Processing helix  chain 'C' and resid 746 through 760
    Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 45
      removed outlier: 8.811A  pdb=" N   PHE B  74 " --> pdb=" O   SER B   7 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   GLY B   9 " --> pdb=" O   PHE B  74 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ILE B  73 " --> pdb=" O   VAL B  97 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   PHE B  96 " --> pdb=" O   ILE B 111 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 164
      removed outlier: 7.447A  pdb=" N   PHE B 133 " --> pdb=" O   THR B 161 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   ILE B 163 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   TYR B 135 " --> pdb=" O   ILE B 163 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   VAL B 134 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   ASP B 192 " --> pdb=" O   VAL B 134 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   LEU B 136 " --> pdb=" O   ASP B 192 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   PHE B 242 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   ILE B 239 " --> pdb=" O   MET B 360 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY B 369 " --> pdb=" O   VAL B 357 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   GLU B 359 " --> pdb=" O   LYS B 367 " (cutoff:3.500A)
      removed outlier: 5.189A  pdb=" N   LYS B 367 " --> pdb=" O   GLU B 359 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   TYR B 370 " --> pdb=" O   VAL B 378 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 49
      removed outlier: 6.445A  pdb=" N   ILE C   6 " --> pdb=" O   ASN C  44 " (cutoff:3.500A)
      removed outlier: 7.895A  pdb=" N   HIS C  46 " --> pdb=" O   ILE C   6 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   ILE C   8 " --> pdb=" O   HIS C  46 " (cutoff:3.500A)
      removed outlier: 8.313A  pdb=" N   ASP C  48 " --> pdb=" O   ILE C   8 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   GLY C  10 " --> pdb=" O   ASP C  48 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   ALA C  72 " --> pdb=" O   SER C   7 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   ILE C  73 " --> pdb=" O   VAL C  97 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 161 through 164
      removed outlier: 6.319A  pdb=" N   TYR C 135 " --> pdb=" O   ILE C 163 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   PHE C 242 " --> pdb=" O   LEU C 219 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   ASN C 221 " --> pdb=" O   PHE C 242 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ILE C 239 " --> pdb=" O   MET C 360 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   MET C 360 " --> pdb=" O   ILE C 239 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ILE C 355 " --> pdb=" O   TRP C 371 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   GLY C 369 " --> pdb=" O   VAL C 357 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   GLU C 359 " --> pdb=" O   LYS C 367 " (cutoff:3.500A)
      removed outlier: 5.546A  pdb=" N   LYS C 367 " --> pdb=" O   GLU C 359 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 335 through 337
      removed outlier: 3.650A  pdb=" N   VAL C 335 " --> pdb=" O   ILE C 342 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 443 through 446
      removed outlier: 6.070A  pdb=" N   VAL C 399 " --> pdb=" O   SER C 445 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ILE C 476 " --> pdb=" O   VAL C 398 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 409 through 410
    Processing sheet with id=AA8, first strand: chain 'C' and resid 492 through 493

    287 hydrogen bonds defined for protein.
    840 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: 1.10

  Time building geometry restraints manager: 0.72 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: 2270
        1.34 -     1.46: 1630
        1.46 -     1.58: 3145
        1.58 -     1.69: 0
        1.69 -     1.81: 61
  Bond restraints: 7106
  Sorted by residual:
  bond pdb=" N   PHE B   2 "
       pdb=" CA  PHE B   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.76e+00
  bond pdb=" CG  PRO C  99 "
       pdb=" CD  PRO C  99 "
    ideal  model  delta    sigma   weight residual
    1.503  1.476  0.027 3.40e-02 8.65e+02 6.37e-01
  bond pdb=" C   VAL B 318 "
       pdb=" N   PRO B 319 "
    ideal  model  delta    sigma   weight residual
    1.326  1.337 -0.011 1.44e-02 4.82e+03 6.06e-01
  bond pdb=" C   VAL B 378 "
       pdb=" N   PRO B 379 "
    ideal  model  delta    sigma   weight residual
    1.329  1.338 -0.008 1.22e-02 6.72e+03 4.59e-01
  bond pdb=" C   ILE C 244 "
       pdb=" O   ILE C 244 "
    ideal  model  delta    sigma   weight residual
    1.245  1.236  0.009 1.41e-02 5.03e+03 4.42e-01
  ... (remaining 7101 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.89: 9251
        0.89 -     1.78: 318
        1.78 -     2.68: 41
        2.68 -     3.57: 18
        3.57 -     4.46: 10
  Bond angle restraints: 9638
  Sorted by residual:
  angle pdb=" N   ILE C 244 "
        pdb=" CA  ILE C 244 "
        pdb=" C   ILE C 244 "
      ideal   model   delta    sigma   weight residual
     113.71  109.77    3.94 9.50e-01 1.11e+00 1.72e+01
  angle pdb=" CA  ILE C 244 "
        pdb=" C   ILE C 244 "
        pdb=" N   VAL C 245 "
      ideal   model   delta    sigma   weight residual
     119.87  116.86    3.01 1.34e+00 5.57e-01 5.06e+00
  angle pdb=" N   GLY B 323 "
        pdb=" CA  GLY B 323 "
        pdb=" C   GLY B 323 "
      ideal   model   delta    sigma   weight residual
     114.66  112.04    2.62 1.24e+00 6.50e-01 4.48e+00
  angle pdb=" N   SER C  52 "
        pdb=" CA  SER C  52 "
        pdb=" CB  SER C  52 "
      ideal   model   delta    sigma   weight residual
     112.78  110.13    2.65 1.53e+00 4.27e-01 3.00e+00
  angle pdb=" CA  LYS B 271 "
        pdb=" CB  LYS B 271 "
        pdb=" CG  LYS B 271 "
      ideal   model   delta    sigma   weight residual
     114.10  117.56   -3.46 2.00e+00 2.50e-01 2.99e+00
  ... (remaining 9633 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 3730
       17.44 -    34.88: 359
       34.88 -    52.32: 80
       52.32 -    69.75: 13
       69.75 -    87.19: 9
  Dihedral angle restraints: 4191
    sinusoidal: 1639
      harmonic: 2552
  Sorted by residual:
  dihedral pdb=" CB  CYS C  63 "
           pdb=" SG  CYS C  63 "
           pdb=" SG  CYS C 312 "
           pdb=" CB  CYS C 312 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -148.14   62.14     1      1.00e+01 1.00e-02 5.11e+01
  dihedral pdb=" CA  TRP C 320 "
           pdb=" C   TRP C 320 "
           pdb=" N   SER C 321 "
           pdb=" CA  SER C 321 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.72  -17.28     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CB  GLU C 291 "
           pdb=" CG  GLU C 291 "
           pdb=" CD  GLU C 291 "
           pdb=" OE1 GLU C 291 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.19  -87.19     1      3.00e+01 1.11e-03 1.01e+01
  ... (remaining 4188 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 625
       0.026 -    0.052: 292
       0.052 -    0.078: 76
       0.078 -    0.104: 36
       0.104 -    0.131: 35
  Chirality restraints: 1064
  Sorted by residual:
  chirality pdb=" CA  VAL C 378 "
            pdb=" N   VAL C 378 "
            pdb=" C   VAL C 378 "
            pdb=" CB  VAL C 378 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.27e-01
  chirality pdb=" CA  ILE C 163 "
            pdb=" N   ILE C 163 "
            pdb=" C   ILE C 163 "
            pdb=" CB  ILE C 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.00e-01
  chirality pdb=" CA  ILE B 342 "
            pdb=" N   ILE B 342 "
            pdb=" C   ILE B 342 "
            pdb=" CB  ILE B 342 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.85e-01
  ... (remaining 1061 not shown)

  Planarity restraints: 1243
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 315 "    0.039 5.00e-02 4.00e+02   5.86e-02 5.50e+00
        pdb=" N   PRO B 316 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO B 316 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 316 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C  98 "    0.027 5.00e-02 4.00e+02   4.02e-02 2.59e+00
        pdb=" N   PRO C  99 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO C  99 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO C  99 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 318 "   -0.020 5.00e-02 4.00e+02   3.01e-02 1.45e+00
        pdb=" N   PRO B 319 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO B 319 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 319 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1240 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 349
        2.73 -     3.27: 6815
        3.27 -     3.82: 10358
        3.82 -     4.36: 12227
        4.36 -     4.90: 22006
  Nonbonded interactions: 51755
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG B 141 "
            pdb=" OD1 ASP B 192 "
     model   vdw
     2.190 3.120
  nonbonded pdb=" OD2 ASP C  51 "
            pdb=" OG  SER C  53 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   GLY C 419 "
            pdb=" NH1 ARG C 422 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" OG  SER C  52 "
            pdb=" OD2 ASP C  78 "
     model   vdw
     2.360 3.040
  nonbonded pdb=" OH  TYR C 128 "
            pdb=" OE2 GLU C 359 "
     model   vdw
     2.382 3.040
  ... (remaining 51750 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             10.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.150
  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:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7108  Z= 0.096
  Angle     :  0.421   4.462   9642  Z= 0.235
  Chirality :  0.039   0.131   1064
  Planarity :  0.003   0.059   1243
  Dihedral  : 14.534  87.193   2545
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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 (0.29), residues: 862
  helix:  1.08 (0.28), residues: 358
  sheet: -1.39 (0.43), residues: 165
  loop : -1.32 (0.31), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  68 
 TYR   0.008   0.001   TYR B  77 
 PHE   0.008   0.001   PHE C 377 
 TRP   0.018   0.001   TRP C 320 
 HIS   0.004   0.000   HIS C  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 7106)
  covalent geometry    : angle       0.42053 ( 9638)
  SS BOND              : bond        0.00067 (    2)
  SS BOND              : angle       0.34355 (    4)
  hydrogen bonds       : bond        0.24032 (  287)
  hydrogen bonds       : angle       6.89864 (  840)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.282 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.0945
  time to fit residues: 9.3326
Evaluate side-chains
  58 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.116752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.098331 restraints weight = 10231.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 2.34
r_work: 0.3032 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.1171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7108  Z= 0.160
  Angle     :  0.481   5.034   9642  Z= 0.261
  Chirality :  0.043   0.126   1064
  Planarity :  0.004   0.047   1243
  Dihedral  :  3.811  19.291    959
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  6.83 %
    Favored  : 92.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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: -0.25 (0.29), residues: 862
  helix:  1.41 (0.27), residues: 359
  sheet: -1.21 (0.43), residues: 165
  loop : -1.30 (0.31), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 422 
 TYR   0.021   0.001   TYR C 295 
 PHE   0.014   0.002   PHE B  23 
 TRP   0.015   0.001   TRP B 259 
 HIS   0.004   0.001   HIS B  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 7106)
  covalent geometry    : angle       0.48056 ( 9638)
  SS BOND              : bond        0.00124 (    2)
  SS BOND              : angle       0.76320 (    4)
  hydrogen bonds       : bond        0.04889 (  287)
  hydrogen bonds       : angle       4.56743 (  840)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.301 
Fit side-chains
REVERT: C  170 ASP cc_start: 0.7623 (t0) cc_final: 0.7397 (t0)
REVERT: C  432 TYR cc_start: 0.8678 (t80) cc_final: 0.8291 (t80)
  outliers start: 4
  outliers final: 2
  residues processed: 65
  average time/residue: 0.1006
  time to fit residues: 8.6641
Evaluate side-chains
  57 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain C residue  207 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   chunk 73 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.117620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.099099 restraints weight = 10143.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 2.34
r_work: 0.3026 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.1401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   7108  Z= 0.169
  Angle     :  0.473   5.830   9642  Z= 0.255
  Chirality :  0.042   0.125   1064
  Planarity :  0.003   0.045   1243
  Dihedral  :  3.846  19.516    959
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 10.11 %
    Favored  : 89.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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: -0.21 (0.29), residues: 862
  helix:  1.47 (0.27), residues: 358
  sheet: -1.06 (0.44), residues: 155
  loop : -1.38 (0.31), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 188 
 TYR   0.014   0.001   TYR B  77 
 PHE   0.016   0.002   PHE B  23 
 TRP   0.018   0.002   TRP B 259 
 HIS   0.003   0.001   HIS C  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 7106)
  covalent geometry    : angle       0.47261 ( 9638)
  SS BOND              : bond        0.00091 (    2)
  SS BOND              : angle       0.72850 (    4)
  hydrogen bonds       : bond        0.04562 (  287)
  hydrogen bonds       : angle       4.32266 (  840)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.274 
Fit side-chains
REVERT: C  170 ASP cc_start: 0.7651 (t0) cc_final: 0.7276 (t0)
  outliers start: 4
  outliers final: 2
  residues processed: 64
  average time/residue: 0.0941
  time to fit residues: 8.1874
Evaluate side-chains
  58 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  355 ILE
Chi-restraints excluded: chain C residue  475 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 82 optimal weight:    0.4980
   chunk 43 optimal weight:    0.5980
   chunk 66 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 18 optimal weight:    0.4980
   chunk 0 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.117177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.098604 restraints weight = 10258.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 2.35
r_work: 0.3031 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.1527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7108  Z= 0.138
  Angle     :  0.448   7.309   9642  Z= 0.240
  Chirality :  0.041   0.124   1064
  Planarity :  0.003   0.050   1243
  Dihedral  :  3.732  18.868    959
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 11.07 %
    Favored  : 87.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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: -0.13 (0.29), residues: 862
  helix:  1.58 (0.28), residues: 358
  sheet: -1.02 (0.44), residues: 155
  loop : -1.41 (0.31), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 188 
 TYR   0.013   0.001   TYR B  77 
 PHE   0.013   0.001   PHE B  23 
 TRP   0.015   0.001   TRP B 259 
 HIS   0.003   0.001   HIS C  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 7106)
  covalent geometry    : angle       0.44761 ( 9638)
  SS BOND              : bond        0.00095 (    2)
  SS BOND              : angle       0.64061 (    4)
  hydrogen bonds       : bond        0.04051 (  287)
  hydrogen bonds       : angle       4.16615 (  840)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.289 
Fit side-chains
REVERT: B  353 TYR cc_start: 0.7678 (OUTLIER) cc_final: 0.6464 (m-80)
REVERT: C  170 ASP cc_start: 0.7648 (t0) cc_final: 0.7235 (t0)
REVERT: C  432 TYR cc_start: 0.8700 (t80) cc_final: 0.8335 (t80)
  outliers start: 12
  outliers final: 6
  residues processed: 66
  average time/residue: 0.0884
  time to fit residues: 7.9930
Evaluate side-chains
  62 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  253 GLN
Chi-restraints excluded: chain B residue  353 TYR
Chi-restraints excluded: chain C residue  113 MET
Chi-restraints excluded: chain C residue  269 GLU
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  475 ASP
Chi-restraints excluded: chain C residue  740 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 43 optimal weight:    0.5980
   chunk 17 optimal weight:    0.4980
   chunk 50 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.9382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.117074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.098718 restraints weight = 10276.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 2.33
r_work: 0.3013 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2876 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.1560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   7108  Z= 0.184
  Angle     :  0.480   6.803   9642  Z= 0.256
  Chirality :  0.042   0.128   1064
  Planarity :  0.003   0.042   1243
  Dihedral  :  3.844  19.954    959
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 12.16 %
    Favored  : 86.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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: -0.25 (0.29), residues: 862
  helix:  1.51 (0.27), residues: 358
  sheet: -1.12 (0.43), residues: 155
  loop : -1.48 (0.30), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 188 
 TYR   0.016   0.001   TYR B  77 
 PHE   0.017   0.002   PHE B  23 
 TRP   0.016   0.001   TRP B 259 
 HIS   0.003   0.001   HIS B  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 7106)
  covalent geometry    : angle       0.47972 ( 9638)
  SS BOND              : bond        0.00102 (    2)
  SS BOND              : angle       0.68086 (    4)
  hydrogen bonds       : bond        0.04486 (  287)
  hydrogen bonds       : angle       4.19886 (  840)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: B  353 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.6714 (m-80)
REVERT: C  170 ASP cc_start: 0.7636 (t0) cc_final: 0.7228 (t0)
  outliers start: 12
  outliers final: 9
  residues processed: 69
  average time/residue: 0.0920
  time to fit residues: 8.6783
Evaluate side-chains
  66 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  253 GLN
Chi-restraints excluded: chain B residue  351 THR
Chi-restraints excluded: chain B residue  353 TYR
Chi-restraints excluded: chain C residue  113 MET
Chi-restraints excluded: chain C residue  269 GLU
Chi-restraints excluded: chain C residue  355 ILE
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  475 ASP
Chi-restraints excluded: chain C residue  738 VAL
Chi-restraints excluded: chain C residue  740 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 81 optimal weight:    0.2980
   chunk 25 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 74 optimal weight:    0.3980
   chunk 33 optimal weight:    0.7980
   chunk 70 optimal weight:    0.6980
   chunk 57 optimal weight:    0.3980
   chunk 67 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.5180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.112226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.093703 restraints weight = 10001.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.2832 rms_B_bonded: 2.22
r_work: 0.2701 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2562 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7108  Z= 0.116
  Angle     :  0.431   7.169   9642  Z= 0.231
  Chirality :  0.040   0.123   1064
  Planarity :  0.003   0.054   1243
  Dihedral  :  3.625  18.234    959
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 12.70 %
    Favored  : 85.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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: -0.07 (0.29), residues: 862
  helix:  1.73 (0.28), residues: 358
  sheet: -1.07 (0.43), residues: 155
  loop : -1.45 (0.30), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 188 
 TYR   0.010   0.001   TYR B  77 
 PHE   0.011   0.001   PHE B  23 
 TRP   0.014   0.001   TRP C 259 
 HIS   0.003   0.001   HIS C  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7106)
  covalent geometry    : angle       0.43140 ( 9638)
  SS BOND              : bond        0.00096 (    2)
  SS BOND              : angle       0.55871 (    4)
  hydrogen bonds       : bond        0.03683 (  287)
  hydrogen bonds       : angle       4.03731 (  840)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.348 
Fit side-chains
REVERT: B  353 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.6225 (m-80)
REVERT: C  170 ASP cc_start: 0.7615 (t0) cc_final: 0.7213 (t0)
  outliers start: 11
  outliers final: 7
  residues processed: 69
  average time/residue: 0.0951
  time to fit residues: 8.8127
Evaluate side-chains
  64 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  253 GLN
Chi-restraints excluded: chain B residue  351 THR
Chi-restraints excluded: chain B residue  353 TYR
Chi-restraints excluded: chain C residue  113 MET
Chi-restraints excluded: chain C residue  269 GLU
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  475 ASP
Chi-restraints excluded: chain C residue  740 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0020
   chunk 61 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 75 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.6188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.111679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.093081 restraints weight = 10088.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 2.24
r_work: 0.2881 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2739 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7108  Z= 0.131
  Angle     :  0.443   7.632   9642  Z= 0.234
  Chirality :  0.041   0.122   1064
  Planarity :  0.003   0.047   1243
  Dihedral  :  3.626  17.832    959
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 12.43 %
    Favored  : 85.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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: -0.08 (0.29), residues: 862
  helix:  1.73 (0.28), residues: 358
  sheet: -1.05 (0.43), residues: 155
  loop : -1.47 (0.31), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 188 
 TYR   0.015   0.001   TYR C 295 
 PHE   0.013   0.001   PHE B  23 
 TRP   0.014   0.001   TRP C 259 
 HIS   0.002   0.001   HIS C  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 7106)
  covalent geometry    : angle       0.44337 ( 9638)
  SS BOND              : bond        0.00089 (    2)
  SS BOND              : angle       0.56916 (    4)
  hydrogen bonds       : bond        0.03855 (  287)
  hydrogen bonds       : angle       4.01963 (  840)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.279 
Fit side-chains
REVERT: B  353 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.6459 (m-80)
REVERT: C  170 ASP cc_start: 0.7745 (t0) cc_final: 0.7341 (t0)
  outliers start: 15
  outliers final: 10
  residues processed: 70
  average time/residue: 0.0909
  time to fit residues: 8.6709
Evaluate side-chains
  68 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  253 GLN
Chi-restraints excluded: chain B residue  351 THR
Chi-restraints excluded: chain B residue  353 TYR
Chi-restraints excluded: chain C residue  113 MET
Chi-restraints excluded: chain C residue  269 GLU
Chi-restraints excluded: chain C residue  338 MET
Chi-restraints excluded: chain C residue  360 MET
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  475 ASP
Chi-restraints excluded: chain C residue  738 VAL
Chi-restraints excluded: chain C residue  740 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0030
   chunk 15 optimal weight:    0.9980
   chunk 78 optimal weight:    0.0030
   chunk 85 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 76 optimal weight:    0.0010
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.3006

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.114569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.096086 restraints weight = 9980.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3056 rms_B_bonded: 2.21
r_work: 0.2935 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2797 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.1889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7108  Z= 0.087
  Angle     :  0.413   8.177   9642  Z= 0.219
  Chirality :  0.040   0.121   1064
  Planarity :  0.003   0.042   1243
  Dihedral  :  3.324  14.794    959
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 14.21 %
    Favored  : 84.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  0.13 (0.29), residues: 862
  helix:  1.92 (0.28), residues: 359
  sheet: -0.92 (0.44), residues: 155
  loop : -1.40 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 376 
 TYR   0.007   0.001   TYR B 370 
 PHE   0.008   0.001   PHE C 267 
 TRP   0.013   0.001   TRP B 259 
 HIS   0.002   0.000   HIS C  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 7106)
  covalent geometry    : angle       0.41263 ( 9638)
  SS BOND              : bond        0.00116 (    2)
  SS BOND              : angle       0.48682 (    4)
  hydrogen bonds       : bond        0.03087 (  287)
  hydrogen bonds       : angle       3.85843 (  840)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.227 
Fit side-chains
  outliers start: 8
  outliers final: 6
  residues processed: 66
  average time/residue: 0.0924
  time to fit residues: 8.3409
Evaluate side-chains
  65 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  113 MET
Chi-restraints excluded: chain C residue  338 MET
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  475 ASP
Chi-restraints excluded: chain C residue  738 VAL
Chi-restraints excluded: chain C residue  740 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 7 optimal weight:    0.3980
   chunk 39 optimal weight:    0.0870
   chunk 72 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0020
   chunk 45 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   overall best weight:    0.3966

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.114116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.095892 restraints weight = 9919.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 2.17
r_work: 0.2910 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2771 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.1898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7108  Z= 0.099
  Angle     :  0.406   6.303   9642  Z= 0.216
  Chirality :  0.040   0.120   1064
  Planarity :  0.003   0.040   1243
  Dihedral  :  3.314  14.271    959
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 14.07 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  0.18 (0.29), residues: 862
  helix:  1.95 (0.28), residues: 359
  sheet: -0.86 (0.44), residues: 155
  loop : -1.39 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 188 
 TYR   0.018   0.001   TYR C 295 
 PHE   0.011   0.001   PHE B  23 
 TRP   0.013   0.001   TRP C 259 
 HIS   0.002   0.001   HIS C  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 7106)
  covalent geometry    : angle       0.40631 ( 9638)
  SS BOND              : bond        0.00066 (    2)
  SS BOND              : angle       0.49155 (    4)
  hydrogen bonds       : bond        0.03310 (  287)
  hydrogen bonds       : angle       3.84756 (  840)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.289 
Fit side-chains
REVERT: C  170 ASP cc_start: 0.7598 (t0) cc_final: 0.7266 (t0)
  outliers start: 7
  outliers final: 6
  residues processed: 67
  average time/residue: 0.0875
  time to fit residues: 8.1456
Evaluate side-chains
  65 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  113 MET
Chi-restraints excluded: chain C residue  338 MET
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  475 ASP
Chi-restraints excluded: chain C residue  738 VAL
Chi-restraints excluded: chain C residue  740 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 75 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 16 optimal weight:    0.3980
   chunk 35 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 83 optimal weight:    0.0670
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.5518

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.111993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.093711 restraints weight = 9966.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 2.18
r_work: 0.2906 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2766 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.1867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7108  Z= 0.119
  Angle     :  0.425   6.364   9642  Z= 0.226
  Chirality :  0.040   0.121   1064
  Planarity :  0.003   0.039   1243
  Dihedral  :  3.426  14.933    959
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 2.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 14.21 %
    Favored  : 84.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  0.12 (0.29), residues: 862
  helix:  1.89 (0.28), residues: 359
  sheet: -0.90 (0.44), residues: 155
  loop : -1.40 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 188 
 TYR   0.011   0.001   TYR B  77 
 PHE   0.012   0.001   PHE B  23 
 TRP   0.013   0.001   TRP C 259 
 HIS   0.002   0.001   HIS B  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7106)
  covalent geometry    : angle       0.42506 ( 9638)
  SS BOND              : bond        0.00066 (    2)
  SS BOND              : angle       0.51406 (    4)
  hydrogen bonds       : bond        0.03612 (  287)
  hydrogen bonds       : angle       3.91272 (  840)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.306 
Fit side-chains
REVERT: C  170 ASP cc_start: 0.7641 (t0) cc_final: 0.7269 (t0)
  outliers start: 8
  outliers final: 7
  residues processed: 66
  average time/residue: 0.0794
  time to fit residues: 7.4167
Evaluate side-chains
  68 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  113 MET
Chi-restraints excluded: chain C residue  338 MET
Chi-restraints excluded: chain C residue  360 MET
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain C residue  475 ASP
Chi-restraints excluded: chain C residue  738 VAL
Chi-restraints excluded: chain C residue  740 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0050
   chunk 1 optimal weight:    0.8980
   chunk 79 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 32 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.6794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.111940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.094064 restraints weight = 9916.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.2914 rms_B_bonded: 2.11
r_work: 0.2790 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2653 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7108  Z= 0.140
  Angle     :  0.442   6.660   9642  Z= 0.235
  Chirality :  0.041   0.121   1064
  Planarity :  0.003   0.039   1243
  Dihedral  :  3.565  15.973    959
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 14.21 %
    Favored  : 84.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  0.02 (0.29), residues: 862
  helix:  1.80 (0.28), residues: 359
  sheet: -0.96 (0.43), residues: 155
  loop : -1.43 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 188 
 TYR   0.014   0.001   TYR B  77 
 PHE   0.014   0.001   PHE B  23 
 TRP   0.014   0.001   TRP C 259 
 HIS   0.003   0.001   HIS B  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 7106)
  covalent geometry    : angle       0.44202 ( 9638)
  SS BOND              : bond        0.00072 (    2)
  SS BOND              : angle       0.56140 (    4)
  hydrogen bonds       : bond        0.03891 (  287)
  hydrogen bonds       : angle       3.97577 (  840)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1868.14 seconds
wall clock time: 32 minutes 44.07 seconds (1964.07 seconds total)