Starting phenix.real_space_refine
on Sat Jun 14 16:43:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8psu_17862/06_2025/8psu_17862.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8psu_17862/06_2025/8psu_17862.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8psu_17862/06_2025/8psu_17862.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8psu_17862/06_2025/8psu_17862.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8psu_17862/06_2025/8psu_17862.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8psu_17862/06_2025/8psu_17862.cif"
  }
  resolution = 3.18
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.003
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: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      29      5.49       5
     S      44      5.16       5
     C    5047      2.51       5
     N    1461      2.21       5
     O    1630      1.98       5
     H    7957      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 16169
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 5035
          Classifications: {'peptide': 316}
          Link IDs: {'PTRANS': 18, 'TRANS': 297}
    Chain: "B"
      Number of atoms: 7974
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 515, 7973
          Classifications: {'peptide': 515}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 493}
      Conformer: "B"
        Number of residues, atoms: 515, 7973
          Classifications: {'peptide': 515}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 493}
          bond proxies already assigned to first conformer: 8044
    Chain: "C"
      Number of atoms: 2233
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 2233
          Classifications: {'peptide': 140}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 134}
    Chain: "V"
      Number of atoms: 440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 440
          Classifications: {'RNA': 14}
          Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 3, 'rna3p_pyr': 6}
          Link IDs: {'rna2p': 5, 'rna3p': 8}
    Chain: "S"
      Number of atoms: 486
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 486
          Classifications: {'RNA': 15}
          Modifications used: {'3*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 6, 'rna3p': 8}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    968  SG  CYS A 161      53.348  48.182  17.600  1.00 42.34           S
  ATOM   2856  SG  CYS A 282      52.801  45.100  15.249  1.00 54.27           S

  Time building chain proxies: 11.97, per 1000 atoms: 0.74
  Number of scatterers: 16169
  At special positions: 0
  Unit cell: (86.9, 97.9, 103.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      44     16.00
     P      29     15.00
     O    1630      8.00
     N    1461      7.00
     C    5047      6.00
     H    7957      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: 4.45
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 501 "
        pdb="ZN    ZN A 501 " - pdb=" ND1 HIS A 284 "
        pdb="ZN    ZN A 501 " - pdb=" NE2 HIS A 296 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 161 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 282 "
      Number of angles added : 2


  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1830

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 9 sheets defined
      47.3% alpha, 12.8% beta
      7 base pairs and 12 stacking pairs defined.
    Time for finding SS restraints: 8.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 112 through 123
    Processing helix  chain 'A' and resid 141 through 157
      removed outlier: 3.679A  pdb=" N   ILE A 145 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 169
      removed outlier: 3.703A  pdb=" N   GLY A 168 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLU A 169 " --> pdb=" O   ALA A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 189
    Processing helix  chain 'A' and resid 223 through 236
      removed outlier: 3.662A  pdb=" N   THR A 235 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   THR A 236 " --> pdb=" O   ALA A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 310
    Processing helix  chain 'A' and resid 312 through 322
      removed outlier: 3.544A  pdb=" N   LEU A 322 " --> pdb=" O   GLU A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 356
      removed outlier: 3.558A  pdb=" N   VAL A 348 " --> pdb=" O   THR A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 374
      removed outlier: 3.947A  pdb=" N   ALA A 363 " --> pdb=" O   ARG A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 387
    Processing helix  chain 'A' and resid 388 through 392
      removed outlier: 3.731A  pdb=" N   ILE A 392 " --> pdb=" O   ALA A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 415
    Processing helix  chain 'B' and resid 1 through 5
      removed outlier: 3.911A  pdb=" N   GLN B   5 " --> pdb=" O   TRP B   2 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 39
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 92 through 104
    Processing helix  chain 'B' and resid 107 through 117
    Processing helix  chain 'B' and resid 130 through 137
    Processing helix  chain 'B' and resid 161 through 183
    Processing helix  chain 'B' and resid 184 through 187
    Processing helix  chain 'B' and resid 191 through 203
    Processing helix  chain 'B' and resid 222 through 234
    Processing helix  chain 'B' and resid 236 through 248
      removed outlier: 3.714A  pdb=" N   VAL B 240 " --> pdb=" O   GLY B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 279
      removed outlier: 4.035A  pdb=" N   LEU B 277 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 311
    Processing helix  chain 'B' and resid 356 through 372
    Processing helix  chain 'B' and resid 376 through 396
    Processing helix  chain 'B' and resid 409 through 413
      removed outlier: 3.906A  pdb=" N   GLY B 413 " --> pdb=" O   THR B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 425
    Processing helix  chain 'B' and resid 429 through 436
      removed outlier: 3.972A  pdb=" N   GLN B 434 " --> pdb=" O   PHE B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 454
      removed outlier: 3.504A  pdb=" N   LYS B 454 " --> pdb=" O   VAL B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 479 through 497
    Processing helix  chain 'B' and resid 506 through 514
    Processing helix  chain 'C' and resid 2 through 8
    Processing helix  chain 'C' and resid 16 through 22
      removed outlier: 3.558A  pdb=" N   HIS C  22 " --> pdb=" O   GLU C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 33 through 40
    Processing helix  chain 'C' and resid 42 through 55
      removed outlier: 3.552A  pdb=" N   ASP C  53 " --> pdb=" O   ASN C  49 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 56 through 59
    Processing helix  chain 'C' and resid 87 through 98
      removed outlier: 3.522A  pdb=" N   GLY C  98 " --> pdb=" O   LEU C  94 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 100 through 107
    Processing sheet with id=AA1, first strand: chain 'A' and resid 136 through 137
      removed outlier: 3.589A  pdb=" N   THR B 293 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 194
      removed outlier: 6.102A  pdb=" N   TRP A 198 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 194
      removed outlier: 6.102A  pdb=" N   TRP A 198 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   SER A 248 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   LEU A 277 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   HIS A 271 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 74 through 80
    Processing sheet with id=AA5, first strand: chain 'B' and resid 124 through 125
    Processing sheet with id=AA6, first strand: chain 'B' and resid 155 through 159
      removed outlier: 3.798A  pdb=" N   ARG B 155 " --> pdb=" O   ARG B 145 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   PHE B 140 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 326 through 329
    Processing sheet with id=AA8, first strand: chain 'B' and resid 477 through 478
    Processing sheet with id=AA9, first strand: chain 'C' and resid 72 through 83
      removed outlier: 7.099A  pdb=" N   LYS C  75 " --> pdb=" O   TYR C 119 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   TYR C 119 " --> pdb=" O   LYS C  75 " (cutoff:3.500A)

    367 hydrogen bonds defined for protein.
    1011 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      17 hydrogen bonds
      34 hydrogen bond angles
      0 basepair planarities
      7 basepair parallelities
      12 stacking parallelities
  Total time for adding SS restraints: 6.40

  Time building geometry restraints manager: 5.38 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: 7935
        1.03 -     1.23: 33
        1.23 -     1.42: 3529
        1.42 -     1.61: 4825
        1.61 -     1.81: 64
  Bond restraints: 16386
  Sorted by residual:
  bond pdb=" C   LEU B 144 "
       pdb=" N   ARG B 145 "
    ideal  model  delta    sigma   weight residual
    1.330  1.281  0.049 1.46e-02 4.69e+03 1.15e+01
  bond pdb=" C   ARG B 145 "
       pdb=" N   ASP B 146 "
    ideal  model  delta    sigma   weight residual
    1.327  1.302  0.025 1.47e-02 4.63e+03 2.94e+00
  bond pdb=" C   VAL B 170 "
       pdb=" O   VAL B 170 "
    ideal  model  delta    sigma   weight residual
    1.237  1.246 -0.010 1.13e-02 7.83e+03 7.17e-01
  bond pdb=" CB  ARG A 189 "
       pdb=" CG  ARG A 189 "
    ideal  model  delta    sigma   weight residual
    1.520  1.542 -0.022 3.00e-02 1.11e+03 5.23e-01
  bond pdb=" C   LEU B 166 "
       pdb=" O   LEU B 166 "
    ideal  model  delta    sigma   weight residual
    1.236  1.245 -0.008 1.15e-02 7.56e+03 5.22e-01
  ... (remaining 16381 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.91: 27081
        0.91 -     1.81: 2298
        1.81 -     2.72: 165
        2.72 -     3.63: 59
        3.63 -     4.53: 9
  Bond angle restraints: 29612
  Sorted by residual:
  angle pdb=" N   ASP A 380 "
        pdb=" CA  ASP A 380 "
        pdb=" CB  ASP A 380 "
      ideal   model   delta    sigma   weight residual
     113.65  110.09    3.56 1.47e+00 4.63e-01 5.87e+00
  angle pdb=" C   PHE B 287 "
        pdb=" N   SER B 288 "
        pdb=" CA  SER B 288 "
      ideal   model   delta    sigma   weight residual
     121.54  125.83   -4.29 1.91e+00 2.74e-01 5.04e+00
  angle pdb=" O   ARG B 145 "
        pdb=" C   ARG B 145 "
        pdb=" N   ASP B 146 "
      ideal   model   delta    sigma   weight residual
     123.22  121.06    2.16 1.14e+00 7.69e-01 3.58e+00
  angle pdb=" CA  ARG B 145 "
        pdb=" C   ARG B 145 "
        pdb=" N   ASP B 146 "
      ideal   model   delta    sigma   weight residual
     116.37  118.68   -2.31 1.23e+00 6.61e-01 3.51e+00
  angle pdb=" CB  ARG A 189 "
        pdb=" CG  ARG A 189 "
        pdb=" CD  ARG A 189 "
      ideal   model   delta    sigma   weight residual
     111.30  115.20   -3.90 2.30e+00 1.89e-01 2.87e+00
  ... (remaining 29607 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 6777
       17.94 -    35.88: 640
       35.88 -    53.82: 234
       53.82 -    71.77: 60
       71.77 -    89.71: 14
  Dihedral angle restraints: 7725
    sinusoidal: 4483
      harmonic: 3242
  Sorted by residual:
  dihedral pdb=" CA  ARG B 394 "
           pdb=" C   ARG B 394 "
           pdb=" N   TYR B 395 "
           pdb=" CA  TYR B 395 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.98  -17.02     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" O4'   U V  10 "
           pdb=" C1'   U V  10 "
           pdb=" N1    U V  10 "
           pdb=" C2    U V  10 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00 -176.52   48.52     1      1.70e+01 3.46e-03 1.12e+01
  dihedral pdb=" CB  GLU A 326 "
           pdb=" CG  GLU A 326 "
           pdb=" CD  GLU A 326 "
           pdb=" OE1 GLU A 326 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.71  -89.71     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 7722 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 871
       0.028 -    0.056: 342
       0.056 -    0.084: 57
       0.084 -    0.112: 44
       0.112 -    0.140: 14
  Chirality restraints: 1328
  Sorted by residual:
  chirality pdb=" CA  ILE B 253 "
            pdb=" N   ILE B 253 "
            pdb=" C   ILE B 253 "
            pdb=" CB  ILE B 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.93e-01
  chirality pdb=" CA  VAL B 417 "
            pdb=" N   VAL B 417 "
            pdb=" C   VAL B 417 "
            pdb=" CB  VAL B 417 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.74e-01
  chirality pdb=" CA  ILE A 199 "
            pdb=" N   ILE A 199 "
            pdb=" C   ILE A 199 "
            pdb=" CB  ILE A 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.37e-01
  ... (remaining 1325 not shown)

  Planarity restraints: 2320
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 161 "   -0.031 5.00e-02 4.00e+02   4.77e-02 3.64e+00
        pdb=" N   PRO B 162 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO B 162 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 162 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A V   4 "    0.021 2.00e-02 2.50e+03   8.36e-03 2.27e+00
        pdb=" N9    A V   4 "   -0.019 2.00e-02 2.50e+03
        pdb=" C8    A V   4 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    A V   4 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5    A V   4 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A V   4 "    0.003 2.00e-02 2.50e+03
        pdb=" N6    A V   4 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    A V   4 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    A V   4 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A V   4 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    A V   4 "   -0.005 2.00e-02 2.50e+03
        pdb=" H8    A V   4 "   -0.001 2.00e-02 2.50e+03
        pdb=" H2    A V   4 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 469 "   -0.022 5.00e-02 4.00e+02   3.40e-02 1.85e+00
        pdb=" N   PRO B 470 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO B 470 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 470 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 2317 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 945
        2.19 -     2.79: 31731
        2.79 -     3.40: 43845
        3.40 -     4.00: 58522
        4.00 -     4.60: 91055
  Nonbonded interactions: 226098
  Sorted by model distance:
  nonbonded pdb=" HH  TYR B 186 "
            pdb=" O   SER B 286 "
     model   vdw
     1.589 2.450
  nonbonded pdb=" OE1 GLU C  89 "
            pdb=" H   GLU C  89 "
     model   vdw
     1.605 2.450
  nonbonded pdb=" O   PHE B 164 "
            pdb=" HG  SER B 168 "
     model   vdw
     1.630 2.450
  nonbonded pdb=" O   GLY A 309 "
            pdb="HH22 ARG B 394 "
     model   vdw
     1.651 2.450
  nonbonded pdb=" HG  SER C 121 "
            pdb=" OD1 ASP C 125 "
     model   vdw
     1.658 2.450
  ... (remaining 226093 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.40 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:             1.220
  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:             0.310
  Extract box with map and model:          0.680
  Check model and map are aligned:         0.130
  Set scattering table:                    0.170
  Process input model:                     55.690
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.090
  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:3.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   61.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
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   0.049   8433  Z= 0.114
  Angle     :  0.446   4.533  11529  Z= 0.235
  Chirality :  0.035   0.140   1328
  Planarity :  0.003   0.048   1376
  Dihedral  : 17.338  89.707   3348
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.18 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 16.45 %
    Favored  : 83.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.28), residues: 965
  helix:  2.19 (0.26), residues: 432
  sheet: -0.05 (0.51), residues: 103
  loop :  0.16 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 346 
 HIS   0.003   0.001   HIS B 208 
 PHE   0.009   0.001   PHE C  44 
 TYR   0.010   0.001   TYR A 403 
 ARG   0.002   0.000   ARG B 461 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13189 (  377)
  hydrogen bonds       : angle       4.92140 ( 1045)
  metal coordination   : bond        0.00597 (    4)
  metal coordination   : angle       0.10238 (    2)
  covalent geometry    : bond        0.00251 ( 8429)
  covalent geometry    : angle       0.44642 (11527)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 1.192 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.6806
  time to fit residues: 78.0551
Evaluate side-chains
  89 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 1.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 41 optimal weight:    0.1980
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 46 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
C   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.114548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.088956 restraints weight = 30468.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.2906 rms_B_bonded: 1.81
r_work: 0.2798 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2676 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2642
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2642 r_free = 0.2642    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2642 r_free = 0.2642    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2642
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.0510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8433  Z= 0.122
  Angle     :  0.464   4.529  11529  Z= 0.243
  Chirality :  0.036   0.156   1328
  Planarity :  0.004   0.049   1376
  Dihedral  : 12.164  73.861   1498
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.38 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 15.73 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.28), residues: 965
  helix:  2.29 (0.26), residues: 434
  sheet:  0.07 (0.52), residues: 103
  loop :  0.14 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 346 
 HIS   0.003   0.001   HIS B 174 
 PHE   0.009   0.001   PHE C  44 
 TYR   0.012   0.001   TYR A 403 
 ARG   0.003   0.000   ARG B 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04234 (  377)
  hydrogen bonds       : angle       4.04263 ( 1045)
  metal coordination   : bond        0.00655 (    4)
  metal coordination   : angle       0.53715 (    2)
  covalent geometry    : bond        0.00280 ( 8429)
  covalent geometry    : angle       0.46426 (11527)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 1.272 
Fit side-chains
REVERT: B  224 ASP cc_start: 0.8467 (m-30) cc_final: 0.8262 (m-30)
REVERT: B  461 ARG cc_start: 0.7796 (tpp80) cc_final: 0.6931 (mpp80)
REVERT: C    3 GLN cc_start: 0.5731 (mm-40) cc_final: 0.5503 (mm110)
REVERT: C   55 ASP cc_start: 0.7710 (t0) cc_final: 0.6778 (m-30)
  outliers start: 4
  outliers final: 3
  residues processed: 102
  average time/residue: 0.6890
  time to fit residues: 89.0850
Evaluate side-chains
  93 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 90
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  404 ASN
Chi-restraints excluded: chain C residue   30 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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 = 0.3202 r_free = 0.3202 target = 0.112868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.087609 restraints weight = 30293.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.2855 rms_B_bonded: 1.76
r_work: 0.2747 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2626 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2626
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2625
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2625
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.0754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8433  Z= 0.162
  Angle     :  0.482   4.604  11529  Z= 0.254
  Chirality :  0.036   0.156   1328
  Planarity :  0.004   0.052   1376
  Dihedral  : 12.214  74.529   1498
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 1.79
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.18 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 15.61 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.27), residues: 965
  helix:  2.08 (0.25), residues: 434
  sheet:  0.06 (0.52), residues: 103
  loop : -0.05 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 346 
 HIS   0.005   0.001   HIS B 174 
 PHE   0.010   0.001   PHE C  44 
 TYR   0.014   0.001   TYR A 403 
 ARG   0.003   0.000   ARG B 353 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04571 (  377)
  hydrogen bonds       : angle       4.04336 ( 1045)
  metal coordination   : bond        0.00904 (    4)
  metal coordination   : angle       0.16845 (    2)
  covalent geometry    : bond        0.00384 ( 8429)
  covalent geometry    : angle       0.48173 (11527)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 1.122 
Fit side-chains
  outliers start: 6
  outliers final: 5
  residues processed: 96
  average time/residue: 0.6855
  time to fit residues: 81.4398
Evaluate side-chains
  95 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  404 ASN
Chi-restraints excluded: chain C residue   30 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 93 optimal weight:    0.5980
   chunk 64 optimal weight:    2.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A 155 GLN
C   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.113486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.088064 restraints weight = 30446.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.2874 rms_B_bonded: 1.78
r_work: 0.2765 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2645 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2630
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2630 r_free = 0.2630    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2630 r_free = 0.2630    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2630
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.0910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8433  Z= 0.144
  Angle     :  0.468   4.576  11529  Z= 0.247
  Chirality :  0.036   0.158   1328
  Planarity :  0.004   0.051   1376
  Dihedral  : 12.212  74.407   1498
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.18 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 15.49 %
    Favored  : 83.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.27), residues: 965
  helix:  2.05 (0.25), residues: 435
  sheet:  0.08 (0.52), residues: 103
  loop : -0.10 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 346 
 HIS   0.004   0.001   HIS B 174 
 PHE   0.009   0.001   PHE C  44 
 TYR   0.013   0.001   TYR A 403 
 ARG   0.002   0.000   ARG B 353 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04237 (  377)
  hydrogen bonds       : angle       3.95304 ( 1045)
  metal coordination   : bond        0.00715 (    4)
  metal coordination   : angle       0.57888 (    2)
  covalent geometry    : bond        0.00339 ( 8429)
  covalent geometry    : angle       0.46838 (11527)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 1.371 
Fit side-chains
REVERT: A  105 LYS cc_start: 0.8364 (mtmt) cc_final: 0.7781 (mttp)
REVERT: A  256 ARG cc_start: 0.8209 (ttm-80) cc_final: 0.7813 (ttm-80)
REVERT: C   13 GLU cc_start: 0.7157 (pt0) cc_final: 0.6817 (pt0)
REVERT: C   88 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7483 (mp10)
REVERT: C  138 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8270 (mt)
  outliers start: 9
  outliers final: 6
  residues processed: 103
  average time/residue: 0.6843
  time to fit residues: 88.1808
Evaluate side-chains
  102 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 1.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  372 SER
Chi-restraints excluded: chain B residue  404 ASN
Chi-restraints excluded: chain C residue   30 SER
Chi-restraints excluded: chain C residue   88 GLN
Chi-restraints excluded: chain C residue  138 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 75 optimal weight:    0.0870
   chunk 14 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
C   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.114851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.089533 restraints weight = 30607.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 1.77
r_work: 0.2829 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2705 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2659
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2659 r_free = 0.2659    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2659 r_free = 0.2659    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2659
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.0943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8433  Z= 0.098
  Angle     :  0.437   4.475  11529  Z= 0.229
  Chirality :  0.035   0.152   1328
  Planarity :  0.003   0.049   1376
  Dihedral  : 12.091  74.258   1498
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.97 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 15.85 %
    Favored  : 83.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.28), residues: 965
  helix:  2.24 (0.26), residues: 436
  sheet:  0.16 (0.53), residues: 103
  loop : -0.02 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A 367 
 PHE   0.008   0.001   PHE C  44 
 TYR   0.011   0.001   TYR A 403 
 ARG   0.002   0.000   ARG C 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03660 (  377)
  hydrogen bonds       : angle       3.79751 ( 1045)
  metal coordination   : bond        0.00424 (    4)
  metal coordination   : angle       0.45721 (    2)
  covalent geometry    : bond        0.00229 ( 8429)
  covalent geometry    : angle       0.43740 (11527)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 1.138 
Fit side-chains
REVERT: A  105 LYS cc_start: 0.8376 (mtmt) cc_final: 0.7715 (mttp)
REVERT: A  263 LYS cc_start: 0.6991 (tttt) cc_final: 0.6741 (ttpt)
REVERT: C   13 GLU cc_start: 0.7248 (pt0) cc_final: 0.6907 (pt0)
REVERT: C   88 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7431 (mp10)
REVERT: C  138 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8207 (mt)
  outliers start: 6
  outliers final: 4
  residues processed: 101
  average time/residue: 0.6910
  time to fit residues: 86.9778
Evaluate side-chains
  99 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 1.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  404 ASN
Chi-restraints excluded: chain C residue   30 SER
Chi-restraints excluded: chain C residue   88 GLN
Chi-restraints excluded: chain C residue  138 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
C   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.114023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.088610 restraints weight = 30526.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 1.78
r_work: 0.2743 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2623 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2623
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2629
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2629 r_free = 0.2629    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2629 r_free = 0.2629    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2629
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.1015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8433  Z= 0.126
  Angle     :  0.455   4.535  11529  Z= 0.239
  Chirality :  0.036   0.158   1328
  Planarity :  0.004   0.049   1376
  Dihedral  : 12.114  74.381   1498
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.18 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 15.38 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.28), residues: 965
  helix:  2.22 (0.26), residues: 435
  sheet:  0.12 (0.52), residues: 103
  loop : -0.07 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 346 
 HIS   0.004   0.001   HIS B 174 
 PHE   0.010   0.001   PHE C  44 
 TYR   0.012   0.001   TYR A 403 
 ARG   0.003   0.000   ARG B 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03955 (  377)
  hydrogen bonds       : angle       3.83679 ( 1045)
  metal coordination   : bond        0.00632 (    4)
  metal coordination   : angle       0.37746 (    2)
  covalent geometry    : bond        0.00299 ( 8429)
  covalent geometry    : angle       0.45494 (11527)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 1.163 
Fit side-chains
REVERT: A  105 LYS cc_start: 0.8356 (mtmt) cc_final: 0.7759 (mttp)
REVERT: A  263 LYS cc_start: 0.7014 (tttt) cc_final: 0.6726 (ttpt)
REVERT: B  127 ASP cc_start: 0.8233 (m-30) cc_final: 0.8019 (m-30)
REVERT: C   13 GLU cc_start: 0.7195 (pt0) cc_final: 0.6866 (pt0)
REVERT: C   55 ASP cc_start: 0.7593 (t0) cc_final: 0.6740 (m-30)
REVERT: C   88 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7453 (mp10)
REVERT: C  138 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8220 (mt)
  outliers start: 8
  outliers final: 6
  residues processed: 102
  average time/residue: 0.6747
  time to fit residues: 86.0295
Evaluate side-chains
  102 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 1.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  372 SER
Chi-restraints excluded: chain B residue  404 ASN
Chi-restraints excluded: chain C residue   30 SER
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain C residue   88 GLN
Chi-restraints excluded: chain C residue  138 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 86 optimal weight:    1.9990
   chunk 66 optimal weight:    0.4980
   chunk 7 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 38 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
C   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.114421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.089131 restraints weight = 30432.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.2889 rms_B_bonded: 1.77
r_work: 0.2783 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2664 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2705
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2705
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.1064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8433  Z= 0.124
  Angle     :  0.452   4.526  11529  Z= 0.237
  Chirality :  0.035   0.156   1328
  Planarity :  0.004   0.049   1376
  Dihedral  : 12.116  74.369   1498
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 2.10
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.38 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 15.61 %
    Favored  : 83.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.28), residues: 965
  helix:  2.23 (0.26), residues: 435
  sheet:  0.12 (0.52), residues: 103
  loop : -0.06 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 346 
 HIS   0.003   0.001   HIS B 174 
 PHE   0.009   0.001   PHE C  44 
 TYR   0.012   0.001   TYR A 403 
 ARG   0.002   0.000   ARG B 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03911 (  377)
  hydrogen bonds       : angle       3.82600 ( 1045)
  metal coordination   : bond        0.00628 (    4)
  metal coordination   : angle       0.48519 (    2)
  covalent geometry    : bond        0.00291 ( 8429)
  covalent geometry    : angle       0.45209 (11527)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 1.353 
Fit side-chains
REVERT: A  105 LYS cc_start: 0.8356 (mtmt) cc_final: 0.7803 (mttp)
REVERT: C   13 GLU cc_start: 0.7167 (pt0) cc_final: 0.6885 (pt0)
REVERT: C   55 ASP cc_start: 0.7582 (t0) cc_final: 0.6805 (m-30)
REVERT: C   88 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7443 (mp10)
REVERT: C  138 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8262 (mt)
  outliers start: 8
  outliers final: 6
  residues processed: 102
  average time/residue: 0.6919
  time to fit residues: 88.7122
Evaluate side-chains
  99 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 1.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  372 SER
Chi-restraints excluded: chain B residue  404 ASN
Chi-restraints excluded: chain C residue   30 SER
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain C residue   88 GLN
Chi-restraints excluded: chain C residue  138 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   chunk 53 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0670
   chunk 75 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 66 optimal weight:    0.0170
   overall best weight:    0.4956

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

Flipped N/Q/H residues before XYZ refinement:
C   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.115938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.090539 restraints weight = 30154.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.2932 rms_B_bonded: 1.79
r_work: 0.2828 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2705 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2656
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2656 r_free = 0.2656    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2656 r_free = 0.2656    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2656
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.1118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8433  Z= 0.088
  Angle     :  0.430   4.435  11529  Z= 0.225
  Chirality :  0.035   0.150   1328
  Planarity :  0.003   0.048   1376
  Dihedral  : 12.035  74.219   1498
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 1.73
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.97 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 15.97 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.28), residues: 965
  helix:  2.40 (0.26), residues: 436
  sheet:  0.23 (0.53), residues: 103
  loop :  0.04 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 346 
 HIS   0.002   0.000   HIS A 367 
 PHE   0.007   0.001   PHE C  44 
 TYR   0.010   0.001   TYR A 403 
 ARG   0.002   0.000   ARG C 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03423 (  377)
  hydrogen bonds       : angle       3.70233 ( 1045)
  metal coordination   : bond        0.00434 (    4)
  metal coordination   : angle       0.35982 (    2)
  covalent geometry    : bond        0.00202 ( 8429)
  covalent geometry    : angle       0.43029 (11527)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 1.275 
Fit side-chains
REVERT: A  105 LYS cc_start: 0.8369 (mtmt) cc_final: 0.7714 (mttp)
REVERT: A  263 LYS cc_start: 0.6824 (tttt) cc_final: 0.6620 (ttpt)
REVERT: B  461 ARG cc_start: 0.7694 (tpp80) cc_final: 0.7454 (ttm110)
REVERT: C   13 GLU cc_start: 0.7339 (pt0) cc_final: 0.7021 (pt0)
REVERT: C   55 ASP cc_start: 0.7578 (t0) cc_final: 0.6771 (m-30)
REVERT: C   88 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7447 (mp10)
REVERT: C  138 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8202 (mt)
  outliers start: 8
  outliers final: 6
  residues processed: 102
  average time/residue: 0.6765
  time to fit residues: 86.6773
Evaluate side-chains
  100 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 1.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  372 SER
Chi-restraints excluded: chain B residue  404 ASN
Chi-restraints excluded: chain C residue   30 SER
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain C residue   88 GLN
Chi-restraints excluded: chain C residue  138 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0770
   chunk 89 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 88 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 46 optimal weight:    0.5980
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
C   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.115920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.090437 restraints weight = 30226.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 1.79
r_work: 0.2761 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2642 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2657
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2657 r_free = 0.2657    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2657 r_free = 0.2657    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2657
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.1163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8433  Z= 0.097
  Angle     :  0.435   4.455  11529  Z= 0.228
  Chirality :  0.035   0.153   1328
  Planarity :  0.003   0.048   1376
  Dihedral  : 12.002  74.255   1498
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.28 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 16.09 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.28), residues: 965
  helix:  2.41 (0.26), residues: 436
  sheet:  0.23 (0.52), residues: 103
  loop :  0.02 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 346 
 HIS   0.002   0.001   HIS A 367 
 PHE   0.008   0.001   PHE C  44 
 TYR   0.011   0.001   TYR A 403 
 ARG   0.002   0.000   ARG C 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03504 (  377)
  hydrogen bonds       : angle       3.72010 ( 1045)
  metal coordination   : bond        0.00436 (    4)
  metal coordination   : angle       0.38255 (    2)
  covalent geometry    : bond        0.00227 ( 8429)
  covalent geometry    : angle       0.43549 (11527)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 1.137 
Fit side-chains
REVERT: A  105 LYS cc_start: 0.8352 (mtmt) cc_final: 0.7689 (mttp)
REVERT: A  256 ARG cc_start: 0.8098 (ttm-80) cc_final: 0.7725 (ttm-80)
REVERT: A  263 LYS cc_start: 0.6885 (tttt) cc_final: 0.6666 (ttpt)
REVERT: A  323 ASP cc_start: 0.8167 (t70) cc_final: 0.7777 (t70)
REVERT: C   13 GLU cc_start: 0.7376 (pt0) cc_final: 0.7063 (pt0)
REVERT: C   55 ASP cc_start: 0.7567 (t0) cc_final: 0.6748 (m-30)
REVERT: C   88 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7463 (mp10)
REVERT: C  138 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8198 (mt)
  outliers start: 7
  outliers final: 5
  residues processed: 100
  average time/residue: 0.6700
  time to fit residues: 84.6035
Evaluate side-chains
  100 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  372 SER
Chi-restraints excluded: chain B residue  404 ASN
Chi-restraints excluded: chain C residue   30 SER
Chi-restraints excluded: chain C residue   88 GLN
Chi-restraints excluded: chain C residue  138 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 36 optimal weight:    0.3980
   chunk 37 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
C   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.116349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.091782 restraints weight = 30341.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 1.70
r_work: 0.2838 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2720 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2709
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2709 r_free = 0.2709    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2709 r_free = 0.2709    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2709
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.1170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8433  Z= 0.117
  Angle     :  0.447   4.513  11529  Z= 0.234
  Chirality :  0.035   0.154   1328
  Planarity :  0.004   0.048   1376
  Dihedral  : 12.019  74.310   1498
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.28 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 16.09 %
    Favored  : 82.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.28), residues: 965
  helix:  2.36 (0.26), residues: 435
  sheet:  0.22 (0.52), residues: 103
  loop : -0.02 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 346 
 HIS   0.003   0.001   HIS B 174 
 PHE   0.009   0.001   PHE C  44 
 TYR   0.012   0.001   TYR A 403 
 ARG   0.002   0.000   ARG B 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03770 (  377)
  hydrogen bonds       : angle       3.77326 ( 1045)
  metal coordination   : bond        0.00611 (    4)
  metal coordination   : angle       0.41425 (    2)
  covalent geometry    : bond        0.00277 ( 8429)
  covalent geometry    : angle       0.44745 (11527)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 1.372 
Fit side-chains
REVERT: A  105 LYS cc_start: 0.8374 (mtmt) cc_final: 0.7760 (mttp)
REVERT: A  263 LYS cc_start: 0.6927 (tttt) cc_final: 0.6708 (ttpt)
REVERT: A  323 ASP cc_start: 0.8168 (t70) cc_final: 0.7800 (t70)
REVERT: C   13 GLU cc_start: 0.7340 (pt0) cc_final: 0.7074 (pt0)
REVERT: C   55 ASP cc_start: 0.7561 (t0) cc_final: 0.6819 (m-30)
REVERT: C   88 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7439 (mp10)
REVERT: C  138 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8249 (mt)
  outliers start: 8
  outliers final: 6
  residues processed: 101
  average time/residue: 0.6359
  time to fit residues: 81.3755
Evaluate side-chains
  102 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  372 SER
Chi-restraints excluded: chain B residue  404 ASN
Chi-restraints excluded: chain C residue   30 SER
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain C residue   88 GLN
Chi-restraints excluded: chain C residue  138 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 80 optimal weight:    0.4980
   chunk 94 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
C   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.116231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.091795 restraints weight = 30240.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 1.69
r_work: 0.2832 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2712 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2693
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2693 r_free = 0.2693    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2693 r_free = 0.2693    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2693
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.1187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8433  Z= 0.107
  Angle     :  0.443   4.485  11529  Z= 0.232
  Chirality :  0.035   0.154   1328
  Planarity :  0.003   0.049   1376
  Dihedral  : 12.014  74.250   1498
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 2.04
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.28 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 16.09 %
    Favored  : 82.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.28), residues: 965
  helix:  2.38 (0.26), residues: 435
  sheet:  0.23 (0.52), residues: 103
  loop :  0.00 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 346 
 HIS   0.003   0.001   HIS B 208 
 PHE   0.009   0.001   PHE C  44 
 TYR   0.011   0.001   TYR A 403 
 ARG   0.002   0.000   ARG C 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03665 (  377)
  hydrogen bonds       : angle       3.77493 ( 1045)
  metal coordination   : bond        0.00505 (    4)
  metal coordination   : angle       0.36092 (    2)
  covalent geometry    : bond        0.00253 ( 8429)
  covalent geometry    : angle       0.44306 (11527)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8927.77 seconds
wall clock time: 152 minutes 0.62 seconds (9120.62 seconds total)