Starting phenix.real_space_refine
on Wed Sep 17 05:41:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kus_62579/09_2025/9kus_62579.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kus_62579/09_2025/9kus_62579.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.42
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kus_62579/09_2025/9kus_62579.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kus_62579/09_2025/9kus_62579.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kus_62579/09_2025/9kus_62579.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kus_62579/09_2025/9kus_62579.map"
  }
  resolution = 3.42
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.017
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      50      5.16       5
     C    3532      2.51       5
     N     898      2.21       5
     O    1008      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 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: 5488
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 355, 2744
          Classifications: {'peptide': 355}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 334}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 355, 2744
          Classifications: {'peptide': 355}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 334}
          Chain breaks: 1
  Time building chain proxies: 1.44, per 1000 atoms: 0.26
  Number of scatterers: 5488
  At special positions: 0
  Unit cell: (102.85, 95.2, 61.2, 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      50     16.00
     O    1008      8.00
     N     898      7.00
     C    3532      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.36
  Conformation dependent library (CDL) restraints added in 177.1 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1316

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 4 sheets defined
      57.9% alpha, 12.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 40
      removed outlier: 3.637A  pdb=" N   PHE A  40 " --> pdb=" O   ILE A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 54
      removed outlier: 3.616A  pdb=" N   ALA A  50 " --> pdb=" O   MET A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 61
      removed outlier: 3.712A  pdb=" N   ILE A  59 " --> pdb=" O   GLN A  55 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA A  61 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 76
    Processing helix  chain 'A' and resid 88 through 103
      removed outlier: 3.723A  pdb=" N   HIS A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 131
    Processing helix  chain 'A' and resid 140 through 144
      removed outlier: 3.641A  pdb=" N   TYR A 143 " --> pdb=" O   LEU A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 161
    Processing helix  chain 'A' and resid 162 through 167
    Processing helix  chain 'A' and resid 168 through 170
      No H-bonds generated for 'chain 'A' and resid 168 through 170'
    Processing helix  chain 'A' and resid 171 through 179
    Processing helix  chain 'A' and resid 181 through 188
    Processing helix  chain 'A' and resid 193 through 197
    Processing helix  chain 'A' and resid 198 through 222
    Processing helix  chain 'A' and resid 226 through 231
      removed outlier: 3.898A  pdb=" N   GLN A 230 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 252
    Processing helix  chain 'A' and resid 262 through 267
      removed outlier: 4.123A  pdb=" N   LYS A 267 " --> pdb=" O   PRO A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 301
    Processing helix  chain 'A' and resid 302 through 317
      removed outlier: 3.565A  pdb=" N   LYS A 315 " --> pdb=" O   LYS A 311 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ALA A 316 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 337
      No H-bonds generated for 'chain 'A' and resid 335 through 337'
    Processing helix  chain 'A' and resid 338 through 350
      removed outlier: 3.697A  pdb=" N   PHE A 342 " --> pdb=" O   GLY A 338 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   MET A 344 " --> pdb=" O   GLY A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 371
    Processing helix  chain 'B' and resid 26 through 40
      removed outlier: 4.332A  pdb=" N   TYR B  32 " --> pdb=" O   GLU B  28 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   PHE B  40 " --> pdb=" O   ILE B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 54
      removed outlier: 3.510A  pdb=" N   MET B  46 " --> pdb=" O   VAL B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 62
      removed outlier: 3.577A  pdb=" N   ILE B  59 " --> pdb=" O   GLN B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 78
    Processing helix  chain 'B' and resid 88 through 103
      removed outlier: 3.660A  pdb=" N   HIS B 103 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 131
    Processing helix  chain 'B' and resid 140 through 144
      removed outlier: 3.584A  pdb=" N   TYR B 143 " --> pdb=" O   LEU B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 161
      removed outlier: 3.502A  pdb=" N   VAL B 160 " --> pdb=" O   LEU B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 167
    Processing helix  chain 'B' and resid 168 through 170
      No H-bonds generated for 'chain 'B' and resid 168 through 170'
    Processing helix  chain 'B' and resid 171 through 179
    Processing helix  chain 'B' and resid 183 through 188
    Processing helix  chain 'B' and resid 193 through 197
    Processing helix  chain 'B' and resid 198 through 222
      removed outlier: 3.583A  pdb=" N   GLU B 203 " --> pdb=" O   PRO B 199 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ASN B 206 " --> pdb=" O   ASN B 202 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   MET B 209 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   LYS B 219 " --> pdb=" O   ILE B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 231
      removed outlier: 3.883A  pdb=" N   GLN B 230 " --> pdb=" O   GLY B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 252
    Processing helix  chain 'B' and resid 262 through 267
      removed outlier: 4.033A  pdb=" N   LYS B 267 " --> pdb=" O   PRO B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 301
      removed outlier: 3.843A  pdb=" N   TRP B 301 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 317
    Processing helix  chain 'B' and resid 335 through 337
      No H-bonds generated for 'chain 'B' and resid 335 through 337'
    Processing helix  chain 'B' and resid 338 through 350
      removed outlier: 3.911A  pdb=" N   MET B 344 " --> pdb=" O   GLY B 340 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLN B 347 " --> pdb=" O   LEU B 343 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   THR B 350 " --> pdb=" O   LEU B 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 371
    Processing sheet with id=AA1, first strand: chain 'A' and resid 106 through 110
    Processing sheet with id=AA2, first strand: chain 'A' and resid 275 through 279
      removed outlier: 7.054A  pdb=" N   ALA A 257 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   VAL A 278 " --> pdb=" O   ALA A 257 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   ASN A 259 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   LYS A 295 " --> pdb=" O   VAL A 237 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   ILE A 292 " --> pdb=" O   ILE A 324 " (cutoff:3.500A)
      removed outlier: 7.679A  pdb=" N   VAL A 326 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   MET A 294 " --> pdb=" O   VAL A 326 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   CYS A 379 " --> pdb=" O   VAL A 386 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   GLU A 388 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 5.625A  pdb=" N   LEU A 377 " --> pdb=" O   GLU A 388 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   TYR A 390 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
      removed outlier: 5.699A  pdb=" N   ILE A 375 " --> pdb=" O   TYR A 390 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 106 through 110
    Processing sheet with id=AA4, first strand: chain 'B' and resid 276 through 279
      removed outlier: 6.712A  pdb=" N   ALA B 257 " --> pdb=" O   GLU B 276 " (cutoff:3.500A)
      removed outlier: 7.664A  pdb=" N   VAL B 278 " --> pdb=" O   ALA B 257 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   ASN B 259 " --> pdb=" O   VAL B 278 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   LEU B 234 " --> pdb=" O   ILE B 258 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   PHE B 260 " --> pdb=" O   LEU B 234 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   ASP B 236 " --> pdb=" O   PHE B 260 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   LYS B 295 " --> pdb=" O   VAL B 237 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ILE B 292 " --> pdb=" O   ILE B 324 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   VAL B 326 " --> pdb=" O   ILE B 292 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   MET B 294 " --> pdb=" O   VAL B 326 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   CYS B 379 " --> pdb=" O   VAL B 386 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   GLU B 388 " --> pdb=" O   LEU B 377 " (cutoff:3.500A)
      removed outlier: 5.590A  pdb=" N   LEU B 377 " --> pdb=" O   GLU B 388 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   TYR B 390 " --> pdb=" O   ILE B 375 " (cutoff:3.500A)
      removed outlier: 5.804A  pdb=" N   ILE B 375 " --> pdb=" O   TYR B 390 " (cutoff:3.500A)

    258 hydrogen bonds defined for protein.
    717 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.62

  Time building geometry restraints manager: 0.47 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1766
        1.35 -     1.46: 1192
        1.46 -     1.58: 2568
        1.58 -     1.70: 0
        1.70 -     1.81: 80
  Bond restraints: 5606
  Sorted by residual:
  bond pdb=" C   ASP B 198 "
       pdb=" O   ASP B 198 "
    ideal  model  delta    sigma   weight residual
    1.249  1.237  0.012 8.50e-03 1.38e+04 1.87e+00
  bond pdb=" CA  HIS B 352 "
       pdb=" CB  HIS B 352 "
    ideal  model  delta    sigma   weight residual
    1.522  1.534 -0.012 1.27e-02 6.20e+03 9.62e-01
  bond pdb=" N   GLY A 188 "
       pdb=" CA  GLY A 188 "
    ideal  model  delta    sigma   weight residual
    1.449  1.462 -0.013 1.45e-02 4.76e+03 8.11e-01
  bond pdb=" C   VAL B 297 "
       pdb=" O   VAL B 297 "
    ideal  model  delta    sigma   weight residual
    1.241  1.232  0.009 1.06e-02 8.90e+03 7.19e-01
  bond pdb=" CB  ASP A 236 "
       pdb=" CG  ASP A 236 "
    ideal  model  delta    sigma   weight residual
    1.516  1.537 -0.021 2.50e-02 1.60e+03 7.15e-01
  ... (remaining 5601 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 7431
        1.72 -     3.44: 132
        3.44 -     5.16: 22
        5.16 -     6.87: 4
        6.87 -     8.59: 1
  Bond angle restraints: 7590
  Sorted by residual:
  angle pdb=" N   LYS A  62 "
        pdb=" CA  LYS A  62 "
        pdb=" C   LYS A  62 "
      ideal   model   delta    sigma   weight residual
     112.57  108.84    3.73 1.13e+00 7.83e-01 1.09e+01
  angle pdb=" CB  MET B 221 "
        pdb=" CG  MET B 221 "
        pdb=" SD  MET B 221 "
      ideal   model   delta    sigma   weight residual
     112.70  121.29   -8.59 3.00e+00 1.11e-01 8.20e+00
  angle pdb=" N   GLY B 321 "
        pdb=" CA  GLY B 321 "
        pdb=" C   GLY B 321 "
      ideal   model   delta    sigma   weight residual
     110.90  114.57   -3.67 1.53e+00 4.27e-01 5.74e+00
  angle pdb=" CA  TYR A 272 "
        pdb=" CB  TYR A 272 "
        pdb=" CG  TYR A 272 "
      ideal   model   delta    sigma   weight residual
     113.90  117.44   -3.54 1.80e+00 3.09e-01 3.86e+00
  angle pdb=" CA  LYS B 256 "
        pdb=" CB  LYS B 256 "
        pdb=" CG  LYS B 256 "
      ideal   model   delta    sigma   weight residual
     114.10  117.90   -3.80 2.00e+00 2.50e-01 3.61e+00
  ... (remaining 7585 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3024
       17.95 -    35.89: 297
       35.89 -    53.84: 63
       53.84 -    71.79: 8
       71.79 -    89.73: 8
  Dihedral angle restraints: 3400
    sinusoidal: 1352
      harmonic: 2048
  Sorted by residual:
  dihedral pdb=" CA  ARG B  84 "
           pdb=" C   ARG B  84 "
           pdb=" N   CYS B  85 "
           pdb=" CA  CYS B  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.95   17.05     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CB  GLU B  53 "
           pdb=" CG  GLU B  53 "
           pdb=" CD  GLU B  53 "
           pdb=" OE1 GLU B  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.73  -89.73     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU B 284 "
           pdb=" CG  GLU B 284 "
           pdb=" CD  GLU B 284 "
           pdb=" OE1 GLU B 284 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.67  -89.67     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 3397 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 499
       0.032 -    0.063: 253
       0.063 -    0.095: 57
       0.095 -    0.127: 44
       0.127 -    0.158: 3
  Chirality restraints: 856
  Sorted by residual:
  chirality pdb=" CB  ILE A 368 "
            pdb=" CA  ILE A 368 "
            pdb=" CG1 ILE A 368 "
            pdb=" CG2 ILE A 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.26e-01
  chirality pdb=" CA  ILE A 323 "
            pdb=" N   ILE A 323 "
            pdb=" C   ILE A 323 "
            pdb=" CB  ILE A 323 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.41e-01
  chirality pdb=" CA  VAL B 145 "
            pdb=" N   VAL B 145 "
            pdb=" C   VAL B 145 "
            pdb=" CB  VAL B 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.25e-01
  ... (remaining 853 not shown)

  Planarity restraints: 972
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 138 "    0.037 5.00e-02 4.00e+02   5.67e-02 5.15e+00
        pdb=" N   PRO B 139 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO B 139 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 139 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 138 "   -0.037 5.00e-02 4.00e+02   5.60e-02 5.02e+00
        pdb=" N   PRO A 139 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A 139 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 139 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 131 "   -0.008 2.00e-02 2.50e+03   1.63e-02 2.64e+00
        pdb=" CG  ASP A 131 "    0.028 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 131 "   -0.010 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 131 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 969 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.82: 1594
        2.82 -     3.34: 5041
        3.34 -     3.86: 8402
        3.86 -     4.38: 9465
        4.38 -     4.90: 16798
  Nonbonded interactions: 41300
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A 361 "
            pdb=" OD1 ASP A 365 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" NE2 GLN B 361 "
            pdb=" OD1 ASP B 365 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" O   LEU A  99 "
            pdb=" OG  SER A 102 "
     model   vdw
     2.411 3.040
  nonbonded pdb=" O   LEU B  99 "
            pdb=" OG  SER B 102 "
     model   vdw
     2.426 3.040
  nonbonded pdb=" N   ASP B  88 "
            pdb=" OD1 ASP B  88 "
     model   vdw
     2.427 3.120
  ... (remaining 41295 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: 0.01
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:             1.000
  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:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.160
  Find NCS groups from input model:        0.070
  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:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
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   0.023   5606  Z= 0.132
  Angle     :  0.605   8.592   7590  Z= 0.334
  Chirality :  0.043   0.158    856
  Planarity :  0.005   0.057    972
  Dihedral  : 15.106  89.731   2084
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 13.17 %
    Favored  : 86.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.32), residues: 702
  helix:  0.39 (0.31), residues: 316
  sheet:  0.64 (0.49), residues: 112
  loop :  1.04 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 328 
 TYR   0.016   0.001   TYR A 390 
 PHE   0.011   0.001   PHE A 216 
 TRP   0.006   0.001   TRP B 385 
 HIS   0.003   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 5606)
  covalent geometry    : angle       0.60494 ( 7590)
  hydrogen bonds       : bond        0.20964 (  258)
  hydrogen bonds       : angle       6.65796 (  717)

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

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

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 108
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A   33 SER cc_start: 0.7748 (t) cc_final: 0.7485 (m)
REVERT: A  383 ASN cc_start: 0.7402 (t0) cc_final: 0.6954 (t0)
REVERT: B   46 MET cc_start: 0.8481 (mmt) cc_final: 0.8122 (mmt)
REVERT: B  251 LYS cc_start: 0.8331 (tttt) cc_final: 0.8111 (ttpt)
REVERT: B  383 ASN cc_start: 0.7396 (t0) cc_final: 0.7064 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 110
  average time/residue: 0.0588
  time to fit residues: 8.9125
Evaluate side-chains
  83 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.4980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.7584

-------------------------------------------------------------------------------
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 = 0.3740 r_free = 0.3740 target = 0.160186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.116625 restraints weight = 6244.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 2.45
r_work: 0.3107 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2932 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5606  Z= 0.121
  Angle     :  0.548  11.565   7590  Z= 0.261
  Chirality :  0.044   0.134    856
  Planarity :  0.006   0.058    972
  Dihedral  :  4.022  16.751    754
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 13.17 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.32), residues: 702
  helix:  0.77 (0.30), residues: 334
  sheet:  1.08 (0.51), residues: 104
  loop :  0.90 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 328 
 TYR   0.018   0.001   TYR B 272 
 PHE   0.012   0.001   PHE B 342 
 TRP   0.005   0.001   TRP A 385 
 HIS   0.003   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 5606)
  covalent geometry    : angle       0.54792 ( 7590)
  hydrogen bonds       : bond        0.04666 (  258)
  hydrogen bonds       : angle       4.82038 (  717)

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

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

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A   33 SER cc_start: 0.7363 (t) cc_final: 0.7146 (m)
REVERT: A  139 PRO cc_start: 0.8331 (Cg_exo) cc_final: 0.8012 (Cg_endo)
REVERT: A  229 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7472 (mm-30)
REVERT: A  282 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7431 (mtp)
REVERT: A  383 ASN cc_start: 0.7497 (t0) cc_final: 0.6946 (t0)
REVERT: B  139 PRO cc_start: 0.8362 (Cg_exo) cc_final: 0.8049 (Cg_endo)
REVERT: B  251 LYS cc_start: 0.8299 (tttt) cc_final: 0.7947 (ttpt)
REVERT: B  264 HIS cc_start: 0.8806 (OUTLIER) cc_final: 0.8284 (t70)
REVERT: B  383 ASN cc_start: 0.7554 (t0) cc_final: 0.7033 (t0)
  outliers start: 12
  outliers final: 4
  residues processed: 93
  average time/residue: 0.0612
  time to fit residues: 8.0616
Evaluate side-chains
  83 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  264 HIS
Chi-restraints excluded: chain B residue  353 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0470
   chunk 40 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    0.1980
   chunk 16 optimal weight:    0.4980
   chunk 6 optimal weight:    0.4980
   overall best weight:    0.3878

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

Flipped N/Q/H residues before XYZ refinement:
B 103 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.163562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.120566 restraints weight = 6158.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 2.42
r_work: 0.3141 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   5606  Z= 0.090
  Angle     :  0.494  12.505   7590  Z= 0.227
  Chirality :  0.041   0.134    856
  Planarity :  0.005   0.055    972
  Dihedral  :  3.680  14.126    754
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 13.83 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.32), residues: 702
  helix:  1.12 (0.29), residues: 340
  sheet:  1.21 (0.52), residues: 104
  loop :  1.05 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 328 
 TYR   0.017   0.001   TYR B 272 
 PHE   0.011   0.001   PHE B 342 
 TRP   0.004   0.000   TRP A 385 
 HIS   0.003   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00189 ( 5606)
  covalent geometry    : angle       0.49424 ( 7590)
  hydrogen bonds       : bond        0.03692 (  258)
  hydrogen bonds       : angle       4.48493 (  717)

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

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

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A  139 PRO cc_start: 0.8274 (Cg_exo) cc_final: 0.8006 (Cg_endo)
REVERT: A  166 MET cc_start: 0.8615 (tpp) cc_final: 0.8238 (mmm)
REVERT: A  282 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7460 (mtp)
REVERT: A  383 ASN cc_start: 0.7319 (t0) cc_final: 0.6679 (t0)
REVERT: B  264 HIS cc_start: 0.8822 (OUTLIER) cc_final: 0.8340 (t70)
REVERT: B  383 ASN cc_start: 0.7528 (t0) cc_final: 0.6956 (t0)
  outliers start: 10
  outliers final: 7
  residues processed: 87
  average time/residue: 0.0590
  time to fit residues: 7.4300
Evaluate side-chains
  85 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  264 HIS
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain B residue  148 GLN
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  264 HIS
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  332 GLU
Chi-restraints excluded: chain B residue  353 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 21 optimal weight:    0.0070
   chunk 62 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0050
   chunk 6 optimal weight:    0.7980
   chunk 11 optimal weight:    0.1980
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.3212

-------------------------------------------------------------------------------
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 = 0.3778 r_free = 0.3778 target = 0.163623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.119624 restraints weight = 6187.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.51
r_work: 0.3142 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   5606  Z= 0.083
  Angle     :  0.505  13.325   7590  Z= 0.225
  Chirality :  0.041   0.133    856
  Planarity :  0.005   0.052    972
  Dihedral  :  3.520  13.032    754
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.50 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.33), residues: 702
  helix:  1.46 (0.29), residues: 340
  sheet:  1.30 (0.52), residues: 104
  loop :  1.11 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 328 
 TYR   0.016   0.001   TYR B 272 
 PHE   0.008   0.001   PHE B 342 
 TRP   0.005   0.001   TRP A 385 
 HIS   0.002   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00173 ( 5606)
  covalent geometry    : angle       0.50470 ( 7590)
  hydrogen bonds       : bond        0.03238 (  258)
  hydrogen bonds       : angle       4.25046 (  717)

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

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

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  166 MET cc_start: 0.8600 (tpp) cc_final: 0.8237 (mmm)
REVERT: A  229 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7559 (mm-30)
REVERT: A  282 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7306 (mtp)
REVERT: A  383 ASN cc_start: 0.7326 (t0) cc_final: 0.6746 (t0)
REVERT: B  264 HIS cc_start: 0.8770 (OUTLIER) cc_final: 0.8349 (t70)
REVERT: B  383 ASN cc_start: 0.7456 (t0) cc_final: 0.6999 (t0)
  outliers start: 9
  outliers final: 5
  residues processed: 80
  average time/residue: 0.0651
  time to fit residues: 7.3115
Evaluate side-chains
  80 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue  148 GLN
Chi-restraints excluded: chain B residue  264 HIS
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  353 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 21 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 20 optimal weight:    8.9990
   chunk 56 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0370
   chunk 58 optimal weight:    8.9990
   overall best weight:    0.8860

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

Flipped N/Q/H residues before XYZ refinement:
A 312 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.158326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.114480 restraints weight = 6341.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 2.48
r_work: 0.3075 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2897 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5606  Z= 0.118
  Angle     :  0.545  14.750   7590  Z= 0.243
  Chirality :  0.043   0.138    856
  Planarity :  0.005   0.054    972
  Dihedral  :  3.670  13.282    754
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 14.50 %
    Favored  : 83.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.32), residues: 702
  helix:  1.55 (0.29), residues: 336
  sheet:  1.32 (0.53), residues: 104
  loop :  0.97 (0.39), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 185 
 TYR   0.017   0.001   TYR B 272 
 PHE   0.005   0.001   PHE A 293 
 TRP   0.010   0.001   TRP B 385 
 HIS   0.003   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 5606)
  covalent geometry    : angle       0.54545 ( 7590)
  hydrogen bonds       : bond        0.04126 (  258)
  hydrogen bonds       : angle       4.21398 (  717)

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

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

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.8513 (mtp85) cc_final: 0.8217 (mmm160)
REVERT: A  282 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7506 (mtp)
REVERT: A  383 ASN cc_start: 0.7506 (t0) cc_final: 0.6819 (t0)
REVERT: B  383 ASN cc_start: 0.7638 (t0) cc_final: 0.7031 (t0)
  outliers start: 11
  outliers final: 9
  residues processed: 79
  average time/residue: 0.0786
  time to fit residues: 8.3553
Evaluate side-chains
  80 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  264 HIS
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  294 MET
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue  148 GLN
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  264 HIS
Chi-restraints excluded: chain B residue  353 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 27 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 45 optimal weight:    0.3980
   chunk 37 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.159376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.115270 restraints weight = 6244.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 2.52
r_work: 0.3087 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5606  Z= 0.106
  Angle     :  0.536  14.916   7590  Z= 0.234
  Chirality :  0.042   0.135    856
  Planarity :  0.005   0.053    972
  Dihedral  :  3.627  13.245    754
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.83 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.98 (0.32), residues: 702
  helix:  1.57 (0.29), residues: 344
  sheet:  1.62 (0.54), residues: 100
  loop :  1.03 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 185 
 TYR   0.016   0.001   TYR B 272 
 PHE   0.005   0.001   PHE A 216 
 TRP   0.007   0.001   TRP A 385 
 HIS   0.003   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 5606)
  covalent geometry    : angle       0.53551 ( 7590)
  hydrogen bonds       : bond        0.03731 (  258)
  hydrogen bonds       : angle       4.14890 (  717)

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

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

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.8527 (mtp85) cc_final: 0.8191 (mmm160)
REVERT: A  229 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7581 (mm-30)
REVERT: A  282 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7398 (mtp)
REVERT: A  383 ASN cc_start: 0.7455 (t0) cc_final: 0.6732 (t0)
REVERT: B  383 ASN cc_start: 0.7580 (t0) cc_final: 0.6991 (t0)
  outliers start: 13
  outliers final: 8
  residues processed: 79
  average time/residue: 0.0711
  time to fit residues: 7.7573
Evaluate side-chains
  78 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue  148 GLN
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  264 HIS
Chi-restraints excluded: chain B residue  353 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 3 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 312 ASN
** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.158665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.114615 restraints weight = 6342.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 2.52
r_work: 0.3086 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2913 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.3006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5606  Z= 0.105
  Angle     :  0.532  14.959   7590  Z= 0.233
  Chirality :  0.042   0.136    856
  Planarity :  0.005   0.054    972
  Dihedral  :  3.610  13.145    754
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.00 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.07 (0.32), residues: 702
  helix:  1.68 (0.29), residues: 344
  sheet:  1.68 (0.54), residues: 100
  loop :  1.01 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 185 
 TYR   0.016   0.001   TYR B 272 
 PHE   0.006   0.001   PHE A 216 
 TRP   0.008   0.001   TRP A 385 
 HIS   0.003   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 5606)
  covalent geometry    : angle       0.53168 ( 7590)
  hydrogen bonds       : bond        0.03701 (  258)
  hydrogen bonds       : angle       4.11280 (  717)

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

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

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.8529 (mtp85) cc_final: 0.8220 (mmm160)
REVERT: A  229 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7560 (mm-30)
REVERT: A  383 ASN cc_start: 0.7510 (t0) cc_final: 0.6786 (t0)
REVERT: B  383 ASN cc_start: 0.7659 (t0) cc_final: 0.7030 (t0)
  outliers start: 13
  outliers final: 12
  residues processed: 82
  average time/residue: 0.0747
  time to fit residues: 8.3286
Evaluate side-chains
  82 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  264 HIS
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue  148 GLN
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  264 HIS
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  380 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0270
   chunk 11 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0980
   chunk 53 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0770
   chunk 3 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.2996

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

Flipped N/Q/H residues before XYZ refinement:
** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.158868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.111972 restraints weight = 6218.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 2.83
r_work: 0.3068 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   5606  Z= 0.077
  Angle     :  0.507  14.200   7590  Z= 0.218
  Chirality :  0.041   0.133    856
  Planarity :  0.005   0.052    972
  Dihedral  :  3.407  13.958    754
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 16.00 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.31 (0.33), residues: 702
  helix:  1.91 (0.29), residues: 344
  sheet:  1.64 (0.54), residues: 100
  loop :  1.15 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 328 
 TYR   0.013   0.001   TYR B 272 
 PHE   0.006   0.001   PHE B 342 
 TRP   0.005   0.001   TRP A 385 
 HIS   0.002   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00163 ( 5606)
  covalent geometry    : angle       0.50741 ( 7590)
  hydrogen bonds       : bond        0.02909 (  258)
  hydrogen bonds       : angle       4.01985 (  717)

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

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

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.8424 (mtp85) cc_final: 0.8041 (mmm160)
REVERT: A  166 MET cc_start: 0.8198 (tpp) cc_final: 0.7859 (mmm)
REVERT: A  229 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7500 (mm-30)
REVERT: A  272 TYR cc_start: 0.6795 (t80) cc_final: 0.6511 (t80)
REVERT: A  282 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.7029 (mtp)
REVERT: A  383 ASN cc_start: 0.7087 (t0) cc_final: 0.6471 (t0)
REVERT: B  383 ASN cc_start: 0.7216 (t0) cc_final: 0.6588 (t0)
  outliers start: 11
  outliers final: 6
  residues processed: 79
  average time/residue: 0.0740
  time to fit residues: 7.7931
Evaluate side-chains
  77 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue  148 GLN
Chi-restraints excluded: chain B residue  264 HIS
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  380 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 40 optimal weight:    0.4980
   chunk 58 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0170
   chunk 13 optimal weight:    0.7980
   chunk 59 optimal weight:    9.9990
   chunk 20 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
A  34 ASN
** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.156368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.109268 restraints weight = 6273.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 2.82
r_work: 0.3052 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   5606  Z= 0.093
  Angle     :  0.533  14.766   7590  Z= 0.229
  Chirality :  0.042   0.135    856
  Planarity :  0.005   0.051    972
  Dihedral  :  3.425  14.019    754
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 16.00 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.21 (0.33), residues: 702
  helix:  1.81 (0.29), residues: 356
  sheet:  1.66 (0.54), residues: 100
  loop :  1.05 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 328 
 TYR   0.014   0.001   TYR B 272 
 PHE   0.006   0.001   PHE B 364 
 TRP   0.007   0.001   TRP B 385 
 HIS   0.003   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 5606)
  covalent geometry    : angle       0.53336 ( 7590)
  hydrogen bonds       : bond        0.03375 (  258)
  hydrogen bonds       : angle       3.99375 (  717)

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

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

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.8464 (mtp85) cc_final: 0.8081 (mmm160)
REVERT: A  229 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7471 (mm-30)
REVERT: A  272 TYR cc_start: 0.6758 (t80) cc_final: 0.6456 (t80)
REVERT: A  282 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6982 (mtp)
REVERT: A  383 ASN cc_start: 0.7225 (t0) cc_final: 0.6552 (t0)
REVERT: B  232 GLU cc_start: 0.7020 (tp30) cc_final: 0.6186 (tm-30)
REVERT: B  276 GLU cc_start: 0.6733 (mm-30) cc_final: 0.6026 (mm-30)
REVERT: B  383 ASN cc_start: 0.7274 (t0) cc_final: 0.6602 (t0)
  outliers start: 8
  outliers final: 7
  residues processed: 77
  average time/residue: 0.0707
  time to fit residues: 7.4657
Evaluate side-chains
  79 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue  148 GLN
Chi-restraints excluded: chain B residue  264 HIS
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  380 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0060
   chunk 3 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0050
   chunk 15 optimal weight:    0.0060
   overall best weight:    0.2826

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

Flipped N/Q/H residues before XYZ refinement:
** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.157196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.112224 restraints weight = 6262.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 2.64
r_work: 0.3077 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.3301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   5606  Z= 0.077
  Angle     :  0.512  14.664   7590  Z= 0.218
  Chirality :  0.041   0.133    856
  Planarity :  0.005   0.050    972
  Dihedral  :  3.314  14.411    754
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 15.67 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.27 (0.33), residues: 702
  helix:  1.91 (0.29), residues: 356
  sheet:  1.61 (0.55), residues: 98
  loop :  1.03 (0.42), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 328 
 TYR   0.013   0.001   TYR B 272 
 PHE   0.006   0.001   PHE B 364 
 TRP   0.005   0.001   TRP A 385 
 HIS   0.002   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00163 ( 5606)
  covalent geometry    : angle       0.51239 ( 7590)
  hydrogen bonds       : bond        0.02935 (  258)
  hydrogen bonds       : angle       3.96960 (  717)

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

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

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1404 Ramachandran restraints generated.
    702 Oldfield, 0 Emsley, 702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A   66 ARG cc_start: 0.8474 (mtp85) cc_final: 0.8065 (mmm160)
REVERT: A  166 MET cc_start: 0.8287 (tpp) cc_final: 0.8067 (mmm)
REVERT: A  229 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7464 (mm-30)
REVERT: A  272 TYR cc_start: 0.6711 (t80) cc_final: 0.6448 (t80)
REVERT: A  282 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6853 (mtp)
REVERT: A  383 ASN cc_start: 0.7136 (t0) cc_final: 0.6564 (t0)
REVERT: B  276 GLU cc_start: 0.6707 (mm-30) cc_final: 0.5990 (mm-30)
REVERT: B  383 ASN cc_start: 0.7243 (t0) cc_final: 0.6574 (t0)
  outliers start: 8
  outliers final: 6
  residues processed: 76
  average time/residue: 0.0772
  time to fit residues: 7.9683
Evaluate side-chains
  76 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue  148 GLN
Chi-restraints excluded: chain B residue  264 HIS
Chi-restraints excluded: chain B residue  353 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0020
   chunk 13 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 23 optimal weight:    0.4980
   chunk 18 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 62 optimal weight:    0.0980
   overall best weight:    0.4788

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

Flipped N/Q/H residues before XYZ refinement:
** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.155726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.110677 restraints weight = 6179.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 2.66
r_work: 0.3062 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.3326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5606  Z= 0.088
  Angle     :  0.536  14.929   7590  Z= 0.231
  Chirality :  0.041   0.134    856
  Planarity :  0.005   0.051    972
  Dihedral  :  3.338  14.348    754
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 15.67 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.30 (0.33), residues: 702
  helix:  1.96 (0.29), residues: 356
  sheet:  1.66 (0.55), residues: 98
  loop :  1.00 (0.42), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 328 
 TYR   0.013   0.001   TYR B 272 
 PHE   0.007   0.001   PHE B 364 
 TRP   0.005   0.001   TRP B 385 
 HIS   0.003   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00199 ( 5606)
  covalent geometry    : angle       0.53600 ( 7590)
  hydrogen bonds       : bond        0.03165 (  258)
  hydrogen bonds       : angle       3.93685 (  717)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1587.07 seconds
wall clock time: 27 minutes 53.68 seconds (1673.68 seconds total)