Starting phenix.real_space_refine
on Wed Feb  4 22:33:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9o97_70244/02_2026/9o97_70244.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9o97_70244/02_2026/9o97_70244.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9o97_70244/02_2026/9o97_70244.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9o97_70244/02_2026/9o97_70244.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9o97_70244/02_2026/9o97_70244.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9o97_70244/02_2026/9o97_70244.cif"
  }
  resolution = 3.1
  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=   0.003 sd=   0.090
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: 6
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     Cl      6      4.86       5
     C    4270      2.51       5
     N    1074      2.21       5
     O    1098      1.98       5
     H    6770      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13258
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 435, 6626
          Classifications: {'peptide': 435}
          Modifications used: {'ACID-GLU': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 415}
    Chain: "B"
      Number of atoms: 6626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 435, 6626
          Classifications: {'peptide': 435}
          Modifications used: {'ACID-GLU': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 415}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CL': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CL': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 2.40, per 1000 atoms: 0.18
  Number of scatterers: 13258
  At special positions: 0
  Unit cell: (80.028, 116.337, 77.805, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      6     17.00
     S      40     16.00
     O    1098      8.00
     N    1074      7.00
     C    4270      6.00
     H    6770      1.00
    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: 0.82
  Conformation dependent library (CDL) restraints added in 295.6 milliseconds
  

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1512

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 0 sheets defined
      86.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 68
      removed outlier: 3.510A  pdb=" N   ALA A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL A  41 " --> pdb=" O   PHE A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 71
      No H-bonds generated for 'chain 'A' and resid 69 through 71'
    Processing helix  chain 'A' and resid 74 through 101
      removed outlier: 3.745A  pdb=" N   SER A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LEU A  89 " --> pdb=" O   CYS A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 105
    Processing helix  chain 'A' and resid 108 through 116
    Processing helix  chain 'A' and resid 123 through 141
      Proline residue:  A 129  - end of helix
    Processing helix  chain 'A' and resid 147 through 167
      removed outlier: 3.540A  pdb=" N   LEU A 163 " --> pdb=" O   GLY A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 191
      removed outlier: 3.670A  pdb=" N   LEU A 178 " --> pdb=" O   ARG A 174 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   PHE A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 203
      removed outlier: 3.641A  pdb=" N   ILE A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 233
      removed outlier: 4.044A  pdb=" N   LYS A 216 " --> pdb=" O   LEU A 212 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   PHE A 232 " --> pdb=" O   MET A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 251
    Processing helix  chain 'A' and resid 252 through 285
      removed outlier: 3.974A  pdb=" N   LEU A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ILE A 257 " --> pdb=" O   TRP A 253 " (cutoff:3.500A)
      Proline residue:  A 267  - end of helix
      removed outlier: 3.854A  pdb=" N   ASP A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ARG A 282 " --> pdb=" O   ASP A 278 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   VAL A 283 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   HIS A 284 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 309
      removed outlier: 3.646A  pdb=" N   PHE A 307 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 313
    Processing helix  chain 'A' and resid 315 through 318
      removed outlier: 3.847A  pdb=" N   ASN A 318 " --> pdb=" O   GLY A 315 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 315 through 318'
    Processing helix  chain 'A' and resid 319 through 325
    Processing helix  chain 'A' and resid 329 through 349
    Processing helix  chain 'A' and resid 356 through 379
    Processing helix  chain 'A' and resid 380 through 383
      removed outlier: 3.521A  pdb=" N   HIS A 383 " --> pdb=" O   PRO A 380 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 380 through 383'
    Processing helix  chain 'A' and resid 385 through 402
      removed outlier: 4.191A  pdb=" N   PHE A 389 " --> pdb=" O   GLU A 385 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ALA A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLY A 395 " --> pdb=" O   ILE A 391 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA A 396 " --> pdb=" O   ALA A 392 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LEU A 397 " --> pdb=" O   GLY A 393 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   LEU A 398 " --> pdb=" O   MET A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 417
    Processing helix  chain 'A' and resid 418 through 420
      No H-bonds generated for 'chain 'A' and resid 418 through 420'
    Processing helix  chain 'A' and resid 421 through 439
    Processing helix  chain 'A' and resid 443 through 462
      removed outlier: 3.786A  pdb=" N   ALA A 462 " --> pdb=" O   ALA A 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 68
      removed outlier: 3.506A  pdb=" N   ALA B  40 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL B  41 " --> pdb=" O   PHE B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 71
      No H-bonds generated for 'chain 'B' and resid 69 through 71'
    Processing helix  chain 'B' and resid 74 through 101
      removed outlier: 3.749A  pdb=" N   SER B  86 " --> pdb=" O   ALA B  82 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LEU B  89 " --> pdb=" O   CYS B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 105
    Processing helix  chain 'B' and resid 108 through 116
    Processing helix  chain 'B' and resid 123 through 141
      Proline residue:  B 129  - end of helix
    Processing helix  chain 'B' and resid 147 through 167
      removed outlier: 3.528A  pdb=" N   LEU B 163 " --> pdb=" O   GLY B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 191
      removed outlier: 3.603A  pdb=" N   LEU B 178 " --> pdb=" O   ARG B 174 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   PHE B 190 " --> pdb=" O   LEU B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 203
      removed outlier: 3.639A  pdb=" N   ILE B 200 " --> pdb=" O   GLY B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 233
      removed outlier: 4.027A  pdb=" N   LYS B 216 " --> pdb=" O   LEU B 212 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   PHE B 232 " --> pdb=" O   MET B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 251
    Processing helix  chain 'B' and resid 252 through 285
      removed outlier: 3.962A  pdb=" N   LEU B 256 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ILE B 257 " --> pdb=" O   TRP B 253 " (cutoff:3.500A)
      Proline residue:  B 267  - end of helix
      removed outlier: 3.858A  pdb=" N   ASP B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ARG B 282 " --> pdb=" O   ASP B 278 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   VAL B 283 " --> pdb=" O   LEU B 279 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   HIS B 284 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 309
      removed outlier: 3.661A  pdb=" N   PHE B 307 " --> pdb=" O   GLY B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 313
    Processing helix  chain 'B' and resid 315 through 318
      removed outlier: 3.862A  pdb=" N   ASN B 318 " --> pdb=" O   GLY B 315 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 315 through 318'
    Processing helix  chain 'B' and resid 319 through 325
    Processing helix  chain 'B' and resid 329 through 349
    Processing helix  chain 'B' and resid 356 through 379
      removed outlier: 3.562A  pdb=" N   MET B 360 " --> pdb=" O   ILE B 356 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 383
      removed outlier: 3.528A  pdb=" N   HIS B 383 " --> pdb=" O   PRO B 380 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 380 through 383'
    Processing helix  chain 'B' and resid 385 through 402
      removed outlier: 4.207A  pdb=" N   PHE B 389 " --> pdb=" O   GLU B 385 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ALA B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLY B 395 " --> pdb=" O   ILE B 391 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ALA B 396 " --> pdb=" O   ALA B 392 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU B 397 " --> pdb=" O   GLY B 393 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   LEU B 398 " --> pdb=" O   MET B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 417
    Processing helix  chain 'B' and resid 418 through 420
      No H-bonds generated for 'chain 'B' and resid 418 through 420'
    Processing helix  chain 'B' and resid 421 through 439
    Processing helix  chain 'B' and resid 443 through 462
      removed outlier: 3.760A  pdb=" N   ALA B 462 " --> pdb=" O   ALA B 458 " (cutoff:3.500A)

    512 hydrogen bonds defined for protein.
    1518 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.14

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6764
        1.03 -     1.23: 8
        1.23 -     1.42: 2660
        1.42 -     1.62: 3890
        1.62 -     1.81: 74
  Bond restraints: 13396
  Sorted by residual:
  bond pdb=" N   LYS B  30 "
       pdb=" CA  LYS B  30 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.10e+00
  bond pdb=" N   LYS A  30 "
       pdb=" CA  LYS A  30 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.99e+00
  bond pdb=" N   LYS A  30 "
       pdb=" H   LYS A  30 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.23e+00
  bond pdb=" N   LYS B  30 "
       pdb=" H   LYS B  30 "
    ideal  model  delta    sigma   weight residual
    0.860  0.889 -0.029 2.00e-02 2.50e+03 2.16e+00
  bond pdb=" N   VAL A 144 "
       pdb=" CA  VAL A 144 "
    ideal  model  delta    sigma   weight residual
    1.474  1.459  0.015 1.57e-02 4.06e+03 9.37e-01
  ... (remaining 13391 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.10: 22584
        1.10 -     2.21: 1664
        2.21 -     3.31: 65
        3.31 -     4.42: 19
        4.42 -     5.52: 4
  Bond angle restraints: 24336
  Sorted by residual:
  angle pdb=" C   PHE A 208 "
        pdb=" CA  PHE A 208 "
        pdb=" CB  PHE A 208 "
      ideal   model   delta    sigma   weight residual
     117.23  111.71    5.52 1.36e+00 5.41e-01 1.65e+01
  angle pdb=" C   PHE B 208 "
        pdb=" CA  PHE B 208 "
        pdb=" CB  PHE B 208 "
      ideal   model   delta    sigma   weight residual
     117.23  111.74    5.49 1.36e+00 5.41e-01 1.63e+01
  angle pdb=" C   ILE B 109 "
        pdb=" CA  ILE B 109 "
        pdb=" CB  ILE B 109 "
      ideal   model   delta    sigma   weight residual
     114.35  111.25    3.10 1.06e+00 8.90e-01 8.55e+00
  angle pdb=" C   ILE A 109 "
        pdb=" CA  ILE A 109 "
        pdb=" CB  ILE A 109 "
      ideal   model   delta    sigma   weight residual
     114.35  111.29    3.06 1.06e+00 8.90e-01 8.32e+00
  angle pdb=" N   VAL B 144 "
        pdb=" CA  VAL B 144 "
        pdb=" C   VAL B 144 "
      ideal   model   delta    sigma   weight residual
     106.21  109.19   -2.98 1.07e+00 8.73e-01 7.78e+00
  ... (remaining 24331 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 5568
       17.99 -    35.99: 406
       35.99 -    53.98: 186
       53.98 -    71.98: 61
       71.98 -    89.97: 17
  Dihedral angle restraints: 6238
    sinusoidal: 3388
      harmonic: 2850
  Sorted by residual:
  dihedral pdb=" CG  ARG B 126 "
           pdb=" CD  ARG B 126 "
           pdb=" NE  ARG B 126 "
           pdb=" CZ  ARG B 126 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -134.00   44.00     2      1.50e+01 4.44e-03 1.03e+01
  dihedral pdb=" CG  ARG A 126 "
           pdb=" CD  ARG A 126 "
           pdb=" NE  ARG A 126 "
           pdb=" CZ  ARG A 126 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -133.80   43.80     2      1.50e+01 4.44e-03 1.02e+01
  dihedral pdb=" CB  MET B 394 "
           pdb=" CG  MET B 394 "
           pdb=" SD  MET B 394 "
           pdb=" CE  MET B 394 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.67   56.67     3      1.50e+01 4.44e-03 9.41e+00
  ... (remaining 6235 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 656
       0.025 -    0.050: 205
       0.050 -    0.074: 139
       0.074 -    0.099: 52
       0.099 -    0.124: 10
  Chirality restraints: 1062
  Sorted by residual:
  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    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  chirality pdb=" CA  ILE A 239 "
            pdb=" N   ILE A 239 "
            pdb=" C   ILE A 239 "
            pdb=" CB  ILE A 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.79e-01
  chirality pdb=" CA  PRO B 206 "
            pdb=" N   PRO B 206 "
            pdb=" C   PRO B 206 "
            pdb=" CB  PRO B 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.40e-01
  ... (remaining 1059 not shown)

  Planarity restraints: 1958
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 149 "   -0.026 5.00e-02 4.00e+02   3.98e-02 2.54e+00
        pdb=" N   PRO B 150 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 150 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 150 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 149 "   -0.026 5.00e-02 4.00e+02   3.97e-02 2.52e+00
        pdb=" N   PRO A 150 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 150 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 150 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 423 "    0.026 5.00e-02 4.00e+02   3.93e-02 2.47e+00
        pdb=" N   PRO A 424 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 424 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 424 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1955 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 567
        2.20 -     2.80: 26473
        2.80 -     3.40: 36989
        3.40 -     4.00: 46788
        4.00 -     4.60: 75818
  Nonbonded interactions: 186635
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 172 "
            pdb=" HG1 THR B 211 "
     model   vdw
     1.599 2.450
  nonbonded pdb=" OE2 GLU A 172 "
            pdb=" HG1 THR A 211 "
     model   vdw
     1.612 2.450
  nonbonded pdb=" O   GLN B 153 "
            pdb="HD21 ASN B 157 "
     model   vdw
     1.667 2.450
  nonbonded pdb=" O   GLN A 153 "
            pdb="HD21 ASN A 157 "
     model   vdw
     1.669 2.450
  nonbonded pdb=" HE  ARG A  64 "
            pdb=" O   GLY A 140 "
     model   vdw
     1.687 2.450
  ... (remaining 186630 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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:             1.820
  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:             0.090
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     11.180
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
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   0.033   6626  Z= 0.134
  Angle     :  0.530   5.523   9000  Z= 0.323
  Chirality :  0.036   0.124   1062
  Planarity :  0.005   0.040   1128
  Dihedral  : 13.585  89.969   2314
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  6.77 %
    Favored  : 92.92 %
  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 are not related in a simple way.
  whole:  2.29 (0.30), residues: 866
  helix:  2.39 (0.21), residues: 640
  sheet:  None (None), residues: 0
  loop : -1.14 (0.43), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 205 
 TYR   0.006   0.001   TYR A  94 
 PHE   0.020   0.001   PHE B 199 
 TRP   0.007   0.001   TRP B 125 
 HIS   0.002   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 6626)
  covalent geometry    : angle       0.52988 ( 9000)
  hydrogen bonds       : bond        0.15447 (  512)
  hydrogen bonds       : angle       5.12991 ( 1518)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A  174 ARG cc_start: 0.7385 (ttm170) cc_final: 0.6630 (ttp-170)
REVERT: A  330 MET cc_start: 0.7276 (tpp) cc_final: 0.6965 (tpp)
REVERT: B  327 ASN cc_start: 0.7327 (m110) cc_final: 0.6954 (m110)
REVERT: B  330 MET cc_start: 0.7259 (tpp) cc_final: 0.6867 (tpp)
  outliers start: 2
  outliers final: 1
  residues processed: 76
  average time/residue: 0.1960
  time to fit residues: 19.3029
Evaluate side-chains
  73 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3546 r_free = 0.3546 target = 0.137547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.109369 restraints weight = 20670.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 1.87
r_work: 0.3061 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2924 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.0553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6626  Z= 0.123
  Angle     :  0.477   4.325   9000  Z= 0.257
  Chirality :  0.037   0.124   1062
  Planarity :  0.005   0.038   1128
  Dihedral  :  4.052  44.940    922
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  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 are not related in a simple way.
  whole:  2.43 (0.30), residues: 866
  helix:  2.48 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.46 (0.44), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 126 
 TYR   0.007   0.001   TYR A 229 
 PHE   0.018   0.001   PHE B 199 
 TRP   0.004   0.001   TRP B 253 
 HIS   0.002   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6626)
  covalent geometry    : angle       0.47658 ( 9000)
  hydrogen bonds       : bond        0.05526 (  512)
  hydrogen bonds       : angle       4.05163 ( 1518)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A  174 ARG cc_start: 0.7381 (ttm170) cc_final: 0.6615 (ttp-170)
REVERT: A  327 ASN cc_start: 0.7027 (m110) cc_final: 0.6811 (m110)
REVERT: A  330 MET cc_start: 0.7252 (tpp) cc_final: 0.6924 (tpp)
REVERT: B  327 ASN cc_start: 0.7244 (m110) cc_final: 0.6841 (m110)
REVERT: B  330 MET cc_start: 0.7239 (tpp) cc_final: 0.6918 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.2099
  time to fit residues: 21.4390
Evaluate side-chains
  75 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 76 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 50 optimal weight:    0.1980
   chunk 24 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 7 optimal weight:    0.1980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3564 r_free = 0.3564 target = 0.139268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.111443 restraints weight = 20682.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 1.86
r_work: 0.3188 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.0867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6626  Z= 0.101
  Angle     :  0.451   4.161   9000  Z= 0.236
  Chirality :  0.036   0.125   1062
  Planarity :  0.004   0.038   1128
  Dihedral  :  3.607  14.203    920
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 2.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  6.15 %
    Favored  : 93.08 %
  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 are not related in a simple way.
  whole:  2.75 (0.30), residues: 866
  helix:  2.74 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.47 (0.44), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 126 
 TYR   0.005   0.001   TYR A 229 
 PHE   0.012   0.001   PHE A 199 
 TRP   0.004   0.001   TRP B 253 
 HIS   0.002   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 6626)
  covalent geometry    : angle       0.45144 ( 9000)
  hydrogen bonds       : bond        0.04529 (  512)
  hydrogen bonds       : angle       3.81626 ( 1518)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A  174 ARG cc_start: 0.7388 (ttm170) cc_final: 0.6618 (ttp-170)
REVERT: A  327 ASN cc_start: 0.7182 (m110) cc_final: 0.6977 (m110)
REVERT: A  330 MET cc_start: 0.7210 (tpp) cc_final: 0.6969 (tpp)
REVERT: B  327 ASN cc_start: 0.7267 (m110) cc_final: 0.6960 (m110)
REVERT: B  330 MET cc_start: 0.7261 (tpp) cc_final: 0.7022 (tpp)
REVERT: B  456 GLN cc_start: 0.6426 (tt0) cc_final: 0.6107 (tt0)
  outliers start: 5
  outliers final: 3
  residues processed: 86
  average time/residue: 0.1822
  time to fit residues: 20.6630
Evaluate side-chains
  76 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  288 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0070
   chunk 30 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.0602

-------------------------------------------------------------------------------
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 = 0.3549 r_free = 0.3549 target = 0.138024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.109537 restraints weight = 20759.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 1.94
r_work: 0.3161 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3023 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.1054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6626  Z= 0.119
  Angle     :  0.460   4.110   9000  Z= 0.242
  Chirality :  0.037   0.125   1062
  Planarity :  0.004   0.039   1128
  Dihedral  :  3.534  13.540    920
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 2.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  6.92 %
    Favored  : 92.46 %
  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 are not related in a simple way.
  whole:  2.76 (0.30), residues: 866
  helix:  2.77 (0.21), residues: 658
  sheet:  None (None), residues: 0
  loop : -1.48 (0.42), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 209 
 TYR   0.007   0.001   TYR B 210 
 PHE   0.015   0.001   PHE B 199 
 TRP   0.004   0.001   TRP B 253 
 HIS   0.003   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6626)
  covalent geometry    : angle       0.46021 ( 9000)
  hydrogen bonds       : bond        0.04718 (  512)
  hydrogen bonds       : angle       3.77023 ( 1518)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A  174 ARG cc_start: 0.7399 (ttm170) cc_final: 0.6589 (ttp-170)
REVERT: A  327 ASN cc_start: 0.7202 (m110) cc_final: 0.6993 (m110)
REVERT: A  330 MET cc_start: 0.7263 (tpp) cc_final: 0.7010 (tpp)
REVERT: B  327 ASN cc_start: 0.7274 (m110) cc_final: 0.7036 (m110)
REVERT: B  330 MET cc_start: 0.7290 (tpp) cc_final: 0.7062 (tpp)
REVERT: B  456 GLN cc_start: 0.6367 (tt0) cc_final: 0.6067 (tt0)
  outliers start: 4
  outliers final: 3
  residues processed: 76
  average time/residue: 0.2014
  time to fit residues: 19.5118
Evaluate side-chains
  74 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  288 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 63 optimal weight:    0.4980
   chunk 27 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.8986

-------------------------------------------------------------------------------
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 = 0.3546 r_free = 0.3546 target = 0.137710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.110145 restraints weight = 20888.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 1.85
r_work: 0.3160 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.1169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6626  Z= 0.107
  Angle     :  0.445   4.074   9000  Z= 0.232
  Chirality :  0.036   0.125   1062
  Planarity :  0.004   0.039   1128
  Dihedral  :  3.465  12.652    920
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 1.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  6.92 %
    Favored  : 92.31 %
  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 are not related in a simple way.
  whole:  2.84 (0.30), residues: 866
  helix:  2.83 (0.21), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.53 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 209 
 TYR   0.006   0.001   TYR A 210 
 PHE   0.012   0.001   PHE A 199 
 TRP   0.004   0.001   TRP A 253 
 HIS   0.002   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 6626)
  covalent geometry    : angle       0.44489 ( 9000)
  hydrogen bonds       : bond        0.04384 (  512)
  hydrogen bonds       : angle       3.67536 ( 1518)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.226 
Fit side-chains
REVERT: A  330 MET cc_start: 0.7288 (tpp) cc_final: 0.7043 (tpp)
REVERT: B  330 MET cc_start: 0.7291 (tpp) cc_final: 0.7058 (tpp)
REVERT: B  456 GLN cc_start: 0.6432 (tt0) cc_final: 0.6152 (tt0)
  outliers start: 5
  outliers final: 3
  residues processed: 72
  average time/residue: 0.2020
  time to fit residues: 18.6522
Evaluate side-chains
  71 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  288 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 29 optimal weight:    0.1980
   chunk 4 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 65 optimal weight:    0.4980
   chunk 78 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 9 optimal weight:    0.4980
   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 = 0.3644 r_free = 0.3644 target = 0.144364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.117035 restraints weight = 20380.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 1.86
r_work: 0.3196 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.1282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6626  Z= 0.104
  Angle     :  0.439   4.065   9000  Z= 0.229
  Chirality :  0.036   0.125   1062
  Planarity :  0.004   0.039   1128
  Dihedral  :  3.418  12.126    920
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 1.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  7.54 %
    Favored  : 91.69 %
  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 are not related in a simple way.
  whole:  2.93 (0.30), residues: 866
  helix:  2.90 (0.21), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.56 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 174 
 TYR   0.006   0.001   TYR B 210 
 PHE   0.013   0.001   PHE A 199 
 TRP   0.004   0.001   TRP A 253 
 HIS   0.002   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 6626)
  covalent geometry    : angle       0.43867 ( 9000)
  hydrogen bonds       : bond        0.04270 (  512)
  hydrogen bonds       : angle       3.64654 ( 1518)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.372 
Fit side-chains
REVERT: A  330 MET cc_start: 0.7248 (tpp) cc_final: 0.6985 (tpp)
REVERT: B  330 MET cc_start: 0.7204 (tpp) cc_final: 0.6990 (tpp)
REVERT: B  456 GLN cc_start: 0.6323 (tt0) cc_final: 0.6064 (tt0)
  outliers start: 5
  outliers final: 3
  residues processed: 73
  average time/residue: 0.2191
  time to fit residues: 20.6187
Evaluate side-chains
  71 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  178 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.3568 r_free = 0.3568 target = 0.139296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.111419 restraints weight = 20732.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 1.88
r_work: 0.3169 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.1365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6626  Z= 0.120
  Angle     :  0.452   4.085   9000  Z= 0.236
  Chirality :  0.037   0.125   1062
  Planarity :  0.004   0.039   1128
  Dihedral  :  3.433  12.052    920
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 1.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  7.69 %
    Favored  : 91.69 %
  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 are not related in a simple way.
  whole:  2.90 (0.30), residues: 866
  helix:  2.88 (0.21), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.56 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 209 
 TYR   0.007   0.001   TYR B 210 
 PHE   0.013   0.001   PHE A 199 
 TRP   0.004   0.001   TRP A 253 
 HIS   0.003   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 6626)
  covalent geometry    : angle       0.45214 ( 9000)
  hydrogen bonds       : bond        0.04509 (  512)
  hydrogen bonds       : angle       3.66502 ( 1518)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.364 
Fit side-chains
REVERT: A  330 MET cc_start: 0.7298 (tpp) cc_final: 0.7021 (tpp)
REVERT: B  174 ARG cc_start: 0.7193 (ttp-170) cc_final: 0.6945 (ttm-80)
REVERT: B  330 MET cc_start: 0.7270 (tpp) cc_final: 0.7027 (tpp)
REVERT: B  456 GLN cc_start: 0.6372 (tt0) cc_final: 0.6094 (tt0)
  outliers start: 4
  outliers final: 3
  residues processed: 76
  average time/residue: 0.2236
  time to fit residues: 21.7037
Evaluate side-chains
  75 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  178 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0370
   chunk 19 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.7060

-------------------------------------------------------------------------------
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 = 0.3585 r_free = 0.3585 target = 0.140797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.112967 restraints weight = 20606.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 1.88
r_work: 0.3182 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6626  Z= 0.098
  Angle     :  0.436   4.118   9000  Z= 0.226
  Chirality :  0.036   0.124   1062
  Planarity :  0.004   0.039   1128
  Dihedral  :  3.362  11.870    920
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  8.00 %
    Favored  : 91.54 %
  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 are not related in a simple way.
  whole:  3.02 (0.30), residues: 866
  helix:  2.94 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.50 (0.44), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 209 
 TYR   0.006   0.001   TYR B 210 
 PHE   0.012   0.001   PHE A 199 
 TRP   0.004   0.001   TRP A 253 
 HIS   0.002   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 6626)
  covalent geometry    : angle       0.43568 ( 9000)
  hydrogen bonds       : bond        0.04089 (  512)
  hydrogen bonds       : angle       3.61421 ( 1518)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 70
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A  330 MET cc_start: 0.7260 (tpp) cc_final: 0.6998 (tpp)
REVERT: B  174 ARG cc_start: 0.7194 (ttp-170) cc_final: 0.6944 (ttm-80)
REVERT: B  330 MET cc_start: 0.7254 (tpp) cc_final: 0.7037 (tpp)
REVERT: B  456 GLN cc_start: 0.6317 (tt0) cc_final: 0.6070 (tt0)
  outliers start: 3
  outliers final: 3
  residues processed: 73
  average time/residue: 0.2087
  time to fit residues: 19.2696
Evaluate side-chains
  73 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 70
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  178 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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 = 0.3560 r_free = 0.3560 target = 0.138594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.110816 restraints weight = 20952.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 1.89
r_work: 0.3142 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.1480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6626  Z= 0.131
  Angle     :  0.461   4.101   9000  Z= 0.241
  Chirality :  0.037   0.124   1062
  Planarity :  0.004   0.039   1128
  Dihedral  :  3.426  12.191    920
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 2.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  8.00 %
    Favored  : 91.54 %
  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 are not related in a simple way.
  whole:  2.87 (0.30), residues: 866
  helix:  2.86 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.63 (0.43), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 403 
 TYR   0.008   0.001   TYR A 210 
 PHE   0.015   0.001   PHE A 199 
 TRP   0.004   0.001   TRP B 253 
 HIS   0.003   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6626)
  covalent geometry    : angle       0.46090 ( 9000)
  hydrogen bonds       : bond        0.04607 (  512)
  hydrogen bonds       : angle       3.66648 ( 1518)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A  330 MET cc_start: 0.7301 (tpp) cc_final: 0.7006 (tpp)
REVERT: B  167 ARG cc_start: 0.7565 (mtm-85) cc_final: 0.7237 (mtt180)
REVERT: B  174 ARG cc_start: 0.7233 (ttp-170) cc_final: 0.6983 (ttm-80)
REVERT: B  330 MET cc_start: 0.7309 (tpp) cc_final: 0.7062 (tpp)
REVERT: B  456 GLN cc_start: 0.6381 (tt0) cc_final: 0.6133 (tt0)
  outliers start: 3
  outliers final: 3
  residues processed: 72
  average time/residue: 0.2455
  time to fit residues: 22.3620
Evaluate side-chains
  72 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  178 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 75 optimal weight:    0.1980
   chunk 0 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.3668 r_free = 0.3668 target = 0.146227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.118554 restraints weight = 20175.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 1.90
r_work: 0.3192 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6626  Z= 0.098
  Angle     :  0.437   4.031   9000  Z= 0.227
  Chirality :  0.036   0.124   1062
  Planarity :  0.004   0.039   1128
  Dihedral  :  3.362  11.995    920
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 2.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  8.15 %
    Favored  : 91.38 %
  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 are not related in a simple way.
  whole:  3.09 (0.30), residues: 866
  helix:  2.98 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.46 (0.44), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 209 
 TYR   0.006   0.001   TYR B 210 
 PHE   0.028   0.001   PHE B 307 
 TRP   0.004   0.001   TRP B 253 
 HIS   0.002   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 6626)
  covalent geometry    : angle       0.43707 ( 9000)
  hydrogen bonds       : bond        0.04069 (  512)
  hydrogen bonds       : angle       3.58872 ( 1518)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A  330 MET cc_start: 0.7209 (tpp) cc_final: 0.6945 (tpp)
REVERT: B  167 ARG cc_start: 0.7439 (mtm-85) cc_final: 0.7106 (mtt180)
REVERT: B  330 MET cc_start: 0.7245 (tpp) cc_final: 0.7011 (tpp)
REVERT: B  456 GLN cc_start: 0.6269 (tt0) cc_final: 0.6031 (tt0)
  outliers start: 3
  outliers final: 2
  residues processed: 76
  average time/residue: 0.2261
  time to fit residues: 22.1580
Evaluate side-chains
  73 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain B residue  103 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.9780

-------------------------------------------------------------------------------
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 = 0.3572 r_free = 0.3572 target = 0.139792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.111525 restraints weight = 20779.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 1.94
r_work: 0.3172 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.1553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6626  Z= 0.111
  Angle     :  0.447   4.151   9000  Z= 0.232
  Chirality :  0.036   0.125   1062
  Planarity :  0.004   0.039   1128
  Dihedral  :  3.369  12.087    920
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 2.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  8.31 %
    Favored  : 91.08 %
  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 are not related in a simple way.
  whole:  3.03 (0.30), residues: 866
  helix:  2.93 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.49 (0.45), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 126 
 TYR   0.006   0.001   TYR B 210 
 PHE   0.020   0.001   PHE B 307 
 TRP   0.004   0.001   TRP A 253 
 HIS   0.003   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 6626)
  covalent geometry    : angle       0.44675 ( 9000)
  hydrogen bonds       : bond        0.04293 (  512)
  hydrogen bonds       : angle       3.60839 ( 1518)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3106.59 seconds
wall clock time: 53 minutes 13.87 seconds (3193.87 seconds total)