Starting phenix.real_space_refine
on Sun Aug 24 02:25:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8psu_17862/08_2025/8psu_17862.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8psu_17862/08_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_17862/08_2025/8psu_17862.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8psu_17862/08_2025/8psu_17862.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8psu_17862/08_2025/8psu_17862.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8psu_17862/08_2025/8psu_17862.cif"
  }
  resolution = 3.18
  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=   0.003
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.00, per 1000 atoms: 0.25
  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: 1.40
  Conformation dependent library (CDL) restraints added in 717.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  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: 2.33
  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: 3.47

  Time building geometry restraints manager: 1.99 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:             0.720
  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:             0.100
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     22.310
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.690
-------------------------------------------------------------------------------
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 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:  1.54 (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
 ARG   0.002   0.000   ARG B 461 
 TYR   0.010   0.001   TYR A 403 
 PHE   0.009   0.001   PHE C  44 
 TRP   0.003   0.001   TRP A 346 
 HIS   0.003   0.001   HIS B 208 

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

*********************** 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  : 0.288 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.3210
  time to fit residues: 36.1622
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  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    8.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0980
   overall best weight:    1.4188

-------------------------------------------------------------------------------
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 = 0.3204 r_free = 0.3204 target = 0.113179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.087945 restraints weight = 30356.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.2910 rms_B_bonded: 1.76
r_work: 0.2803 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2682 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2619
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2619 r_free = 0.2619    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2619 r_free = 0.2619    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2619
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.0562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8433  Z= 0.164
  Angle     :  0.491   4.628  11529  Z= 0.258
  Chirality :  0.037   0.163   1328
  Planarity :  0.004   0.050   1376
  Dihedral  : 12.241  74.015   1498
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 2.10
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.28 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 15.97 %
    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 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:  1.46 (0.28), residues: 965
  helix:  2.14 (0.26), residues: 434
  sheet:  0.01 (0.52), residues: 103
  loop :  0.06 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 247 
 TYR   0.013   0.001   TYR A 403 
 PHE   0.010   0.001   PHE C  44 
 TRP   0.005   0.001   TRP A 346 
 HIS   0.004   0.001   HIS B 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 8429)
  covalent geometry    : angle       0.49098 (11527)
  hydrogen bonds       : bond        0.04704 (  377)
  hydrogen bonds       : angle       4.12853 ( 1045)
  metal coordination   : bond        0.00901 (    4)
  metal coordination   : angle       0.48770 (    2)

*********************** 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
  100 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 0.395 
Fit side-chains
REVERT: B  218 ASN cc_start: 0.8465 (m-40) cc_final: 0.8248 (m-40)
  outliers start: 5
  outliers final: 4
  residues processed: 98
  average time/residue: 0.3297
  time to fit residues: 39.9698
Evaluate side-chains
  94 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 90
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
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  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 39 optimal weight:    0.0570
   chunk 4 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.7700

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

Flipped N/Q/H residues before XYZ refinement:
B 389 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 = 0.3226 r_free = 0.3226 target = 0.114741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.089381 restraints weight = 30495.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.2892 rms_B_bonded: 1.78
r_work: 0.2783 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2661 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2661
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2676
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2676
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.0710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8433  Z= 0.107
  Angle     :  0.447   4.508  11529  Z= 0.234
  Chirality :  0.035   0.155   1328
  Planarity :  0.003   0.049   1376
  Dihedral  : 12.146  74.277   1498
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 1.67
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  1.87 %
    Favored  : 97.93 %
  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 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:  1.52 (0.28), residues: 965
  helix:  2.21 (0.26), residues: 435
  sheet:  0.11 (0.52), residues: 103
  loop :  0.04 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 353 
 TYR   0.012   0.001   TYR A 403 
 PHE   0.009   0.001   PHE C  44 
 TRP   0.005   0.001   TRP A 346 
 HIS   0.003   0.001   HIS B 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 8429)
  covalent geometry    : angle       0.44661 (11527)
  hydrogen bonds       : bond        0.03963 (  377)
  hydrogen bonds       : angle       3.91356 ( 1045)
  metal coordination   : bond        0.00503 (    4)
  metal coordination   : angle       0.24426 (    2)

*********************** 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
  98 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
REVERT: B  218 ASN cc_start: 0.8430 (m-40) cc_final: 0.8207 (m-40)
REVERT: B  461 ARG cc_start: 0.7805 (tpp80) cc_final: 0.6988 (mpp80)
REVERT: C    3 GLN cc_start: 0.5847 (mm-40) cc_final: 0.5646 (mm110)
REVERT: C   55 ASP cc_start: 0.7691 (t0) cc_final: 0.6894 (m-30)
  outliers start: 4
  outliers final: 3
  residues processed: 96
  average time/residue: 0.3698
  time to fit residues: 43.5899
Evaluate side-chains
  95 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 92
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 16 optimal weight:    0.4980
   chunk 88 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.3225 r_free = 0.3225 target = 0.114642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.089427 restraints weight = 30305.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.2886 rms_B_bonded: 1.77
r_work: 0.2777 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2657 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2657
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2681
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2681 r_free = 0.2681    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2681 r_free = 0.2681    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2681
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.0806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8433  Z= 0.113
  Angle     :  0.447   4.508  11529  Z= 0.234
  Chirality :  0.035   0.153   1328
  Planarity :  0.004   0.049   1376
  Dihedral  : 12.100  74.318   1498
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 1.67
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  1.97 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 15.14 %
    Favored  : 84.03 %
  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:  1.52 (0.28), residues: 965
  helix:  2.24 (0.26), residues: 435
  sheet:  0.12 (0.53), residues: 103
  loop : -0.01 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 247 
 TYR   0.012   0.001   TYR A 403 
 PHE   0.009   0.001   PHE C  44 
 TRP   0.005   0.001   TRP A 346 
 HIS   0.003   0.001   HIS B 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 8429)
  covalent geometry    : angle       0.44655 (11527)
  hydrogen bonds       : bond        0.03883 (  377)
  hydrogen bonds       : angle       3.84535 ( 1045)
  metal coordination   : bond        0.00549 (    4)
  metal coordination   : angle       0.24762 (    2)

*********************** 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
  101 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 94
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
REVERT: B  218 ASN cc_start: 0.8353 (m-40) cc_final: 0.8060 (m-40)
REVERT: C   88 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7484 (mp10)
REVERT: C  138 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8258 (mt)
  outliers start: 7
  outliers final: 4
  residues processed: 99
  average time/residue: 0.3655
  time to fit residues: 44.4886
Evaluate side-chains
  98 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 85 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
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 = 0.3214 r_free = 0.3214 target = 0.113889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.088481 restraints weight = 30448.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 1.80
r_work: 0.2788 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2667 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2621
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2621 r_free = 0.2621    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2621 r_free = 0.2621    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2621
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.0907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8433  Z= 0.133
  Angle     :  0.460   4.546  11529  Z= 0.241
  Chirality :  0.036   0.154   1328
  Planarity :  0.004   0.050   1376
  Dihedral  : 12.124  74.399   1498
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.28 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 15.85 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.28), residues: 965
  helix:  2.18 (0.25), residues: 435
  sheet:  0.07 (0.52), residues: 103
  loop : -0.06 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 155 
 TYR   0.013   0.001   TYR A 403 
 PHE   0.009   0.001   PHE C  44 
 TRP   0.005   0.001   TRP A 346 
 HIS   0.004   0.001   HIS B 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8429)
  covalent geometry    : angle       0.46023 (11527)
  hydrogen bonds       : bond        0.04077 (  377)
  hydrogen bonds       : angle       3.87092 ( 1045)
  metal coordination   : bond        0.00685 (    4)
  metal coordination   : angle       0.34924 (    2)

*********************** 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: 7
    poor density    : 96
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 LYS cc_start: 0.8410 (mtmt) cc_final: 0.7730 (mttp)
REVERT: B  104 LYS cc_start: 0.8439 (mttp) cc_final: 0.8045 (mttm)
REVERT: C   13 GLU cc_start: 0.7272 (pt0) cc_final: 0.6995 (pt0)
REVERT: C   88 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7476 (mp10)
REVERT: C  138 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8213 (mt)
  outliers start: 7
  outliers final: 5
  residues processed: 100
  average time/residue: 0.3777
  time to fit residues: 46.4994
Evaluate side-chains
  101 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 94
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
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 B residue  462 LEU
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 6 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0770
   chunk 21 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.9142

-------------------------------------------------------------------------------
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 = 0.3249 r_free = 0.3249 target = 0.116186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.091613 restraints weight = 30256.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.2942 rms_B_bonded: 1.69
r_work: 0.2834 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2717 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2689
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2689 r_free = 0.2689    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2689 r_free = 0.2689    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2689
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.0971

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= 0.116
  Angle     :  0.447   4.511  11529  Z= 0.235
  Chirality :  0.035   0.155   1328
  Planarity :  0.004   0.049   1376
  Dihedral  : 12.092  74.331   1498
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.28 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 15.85 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.49 (0.28), residues: 965
  helix:  2.22 (0.26), residues: 436
  sheet:  0.10 (0.52), residues: 103
  loop : -0.04 (0.30), residues: 426

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8429)
  covalent geometry    : angle       0.44715 (11527)
  hydrogen bonds       : bond        0.03853 (  377)
  hydrogen bonds       : angle       3.81136 ( 1045)
  metal coordination   : bond        0.00587 (    4)
  metal coordination   : angle       0.31105 (    2)

*********************** 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: 7
    poor density    : 97
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 LYS cc_start: 0.8370 (mtmt) cc_final: 0.7752 (mttp)
REVERT: C   13 GLU cc_start: 0.7196 (pt0) cc_final: 0.6918 (pt0)
REVERT: C   55 ASP cc_start: 0.7629 (t0) cc_final: 0.6893 (m-30)
REVERT: C   88 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7428 (mp10)
REVERT: C  138 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8252 (mt)
  outliers start: 7
  outliers final: 5
  residues processed: 102
  average time/residue: 0.3318
  time to fit residues: 41.7543
Evaluate side-chains
  101 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 94
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 = 0.3217 r_free = 0.3217 target = 0.114023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.089173 restraints weight = 30281.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.2922 rms_B_bonded: 1.72
r_work: 0.2814 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2696 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2666
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2666 r_free = 0.2666    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2666 r_free = 0.2666    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2666
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.1052

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= 0.155
  Angle     :  0.473   4.576  11529  Z= 0.249
  Chirality :  0.036   0.159   1328
  Planarity :  0.004   0.051   1376
  Dihedral  : 12.161  74.489   1498
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.49 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 16.21 %
    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 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:  1.33 (0.27), residues: 965
  helix:  2.11 (0.25), residues: 435
  sheet:  0.01 (0.51), residues: 103
  loop : -0.13 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 155 
 TYR   0.014   0.001   TYR A 403 
 PHE   0.010   0.001   PHE C  44 
 TRP   0.006   0.001   TRP A 346 
 HIS   0.005   0.001   HIS B 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 8429)
  covalent geometry    : angle       0.47324 (11527)
  hydrogen bonds       : bond        0.04309 (  377)
  hydrogen bonds       : angle       3.91142 ( 1045)
  metal coordination   : bond        0.00810 (    4)
  metal coordination   : angle       0.33271 (    2)

*********************** 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
  105 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.482 
Fit side-chains
REVERT: A  105 LYS cc_start: 0.8365 (mtmt) cc_final: 0.7821 (mttp)
REVERT: A  263 LYS cc_start: 0.7087 (tttt) cc_final: 0.6829 (ttpt)
REVERT: C   13 GLU cc_start: 0.7358 (pt0) cc_final: 0.7075 (pt0)
REVERT: C   55 ASP cc_start: 0.7552 (t0) cc_final: 0.6808 (m-30)
REVERT: C   88 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7439 (mp10)
REVERT: C  138 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8270 (mt)
  outliers start: 7
  outliers final: 5
  residues processed: 103
  average time/residue: 0.2824
  time to fit residues: 36.6731
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  : 0.443 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    1.4986

-------------------------------------------------------------------------------
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 = 0.3218 r_free = 0.3218 target = 0.113871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.089326 restraints weight = 30455.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 1.72
r_work: 0.2770 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2654 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2654
-------------------------------------------------------------------------------
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 = 0.35   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 = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2656
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.1150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8433  Z= 0.168
  Angle     :  0.485   4.623  11529  Z= 0.256
  Chirality :  0.037   0.161   1328
  Planarity :  0.004   0.052   1376
  Dihedral  : 12.233  74.497   1498
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 2.10
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.49 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 16.69 %
    Favored  : 82.36 %
  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:  1.22 (0.27), residues: 965
  helix:  2.02 (0.25), residues: 435
  sheet: -0.02 (0.51), residues: 103
  loop : -0.19 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 155 
 TYR   0.014   0.001   TYR A 403 
 PHE   0.010   0.001   PHE C  44 
 TRP   0.005   0.001   TRP A 346 
 HIS   0.005   0.001   HIS B 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 8429)
  covalent geometry    : angle       0.48512 (11527)
  hydrogen bonds       : bond        0.04449 (  377)
  hydrogen bonds       : angle       3.98175 ( 1045)
  metal coordination   : bond        0.00911 (    4)
  metal coordination   : angle       0.52876 (    2)

*********************** 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
  99 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.422 
Fit side-chains
REVERT: A  105 LYS cc_start: 0.8339 (mtmt) cc_final: 0.7783 (mttp)
REVERT: B  461 ARG cc_start: 0.7742 (tpp80) cc_final: 0.7496 (ttm110)
REVERT: C   13 GLU cc_start: 0.7395 (pt0) cc_final: 0.7121 (pt0)
REVERT: C   55 ASP cc_start: 0.7575 (t0) cc_final: 0.6799 (m-30)
REVERT: C   88 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7439 (mp10)
REVERT: C  138 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8259 (mt)
  outliers start: 8
  outliers final: 6
  residues processed: 97
  average time/residue: 0.3078
  time to fit residues: 37.0648
Evaluate side-chains
  98 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
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 87 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0980
   chunk 55 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 1 optimal weight:    0.2980
   chunk 0 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3255 r_free = 0.3255 target = 0.116657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.092134 restraints weight = 30208.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 1.70
r_work: 0.2837 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2716 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2716
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2716
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.1140

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= 0.088
  Angle     :  0.435   4.437  11529  Z= 0.228
  Chirality :  0.035   0.149   1328
  Planarity :  0.003   0.048   1376
  Dihedral  : 12.092  74.177   1498
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.97 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 16.81 %
    Favored  : 82.24 %
  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:  1.55 (0.28), residues: 965
  helix:  2.32 (0.26), residues: 435
  sheet:  0.16 (0.52), residues: 103
  loop : -0.07 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 111 
 TYR   0.010   0.001   TYR A 403 
 PHE   0.007   0.001   PHE A 313 
 TRP   0.005   0.001   TRP A 346 
 HIS   0.002   0.000   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 8429)
  covalent geometry    : angle       0.43537 (11527)
  hydrogen bonds       : bond        0.03509 (  377)
  hydrogen bonds       : angle       3.76392 ( 1045)
  metal coordination   : bond        0.00460 (    4)
  metal coordination   : angle       0.23248 (    2)

*********************** 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
  108 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 LYS cc_start: 0.8296 (mtmt) cc_final: 0.7724 (mttp)
REVERT: A  323 ASP cc_start: 0.8125 (t70) cc_final: 0.7782 (t70)
REVERT: B  461 ARG cc_start: 0.7728 (tpp80) cc_final: 0.7496 (ttm110)
REVERT: C   13 GLU cc_start: 0.7403 (pt0) cc_final: 0.7140 (pt0)
REVERT: C   55 ASP cc_start: 0.7568 (t0) cc_final: 0.6861 (m-30)
REVERT: C   88 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7461 (mp10)
REVERT: C  138 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8237 (mt)
  outliers start: 8
  outliers final: 6
  residues processed: 105
  average time/residue: 0.3192
  time to fit residues: 41.9237
Evaluate side-chains
  106 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
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 12 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 64 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3218 r_free = 0.3218 target = 0.114035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.089018 restraints weight = 30355.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 1.74
r_work: 0.2795 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2678 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2689
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2689 r_free = 0.2689    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2689 r_free = 0.2689    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2689
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.1186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8433  Z= 0.147
  Angle     :  0.470   4.560  11529  Z= 0.247
  Chirality :  0.036   0.158   1328
  Planarity :  0.004   0.050   1376
  Dihedral  : 12.137  74.380   1498
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.49 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 16.92 %
    Favored  : 82.12 %
  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:  1.37 (0.28), residues: 965
  helix:  2.18 (0.26), residues: 435
  sheet:  0.06 (0.51), residues: 103
  loop : -0.17 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 155 
 TYR   0.013   0.001   TYR A 403 
 PHE   0.010   0.001   PHE C  44 
 TRP   0.005   0.001   TRP A 346 
 HIS   0.004   0.001   HIS B 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 8429)
  covalent geometry    : angle       0.46959 (11527)
  hydrogen bonds       : bond        0.04132 (  377)
  hydrogen bonds       : angle       3.90391 ( 1045)
  metal coordination   : bond        0.00843 (    4)
  metal coordination   : angle       0.33497 (    2)

********************** 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  : 0.376 
Fit side-chains
REVERT: A  105 LYS cc_start: 0.8309 (mtmt) cc_final: 0.7749 (mttp)
REVERT: C   55 ASP cc_start: 0.7534 (t0) cc_final: 0.6804 (m-30)
REVERT: C   88 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7456 (mp10)
REVERT: C  138 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8258 (mt)
  outliers start: 8
  outliers final: 6
  residues processed: 101
  average time/residue: 0.3464
  time to fit residues: 42.8157
Evaluate side-chains
  101 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
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 55 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 66 optimal weight:    0.2980
   chunk 15 optimal weight:    0.2980
   chunk 18 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 87 optimal weight:    0.2980
   overall best weight:    0.5382

-------------------------------------------------------------------------------
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 = 0.3266 r_free = 0.3266 target = 0.117471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.093046 restraints weight = 30164.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.2941 rms_B_bonded: 1.69
r_work: 0.2834 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2704
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2704 r_free = 0.2704    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2704 r_free = 0.2704    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2704
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.1192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8433  Z= 0.095
  Angle     :  0.440   4.448  11529  Z= 0.231
  Chirality :  0.035   0.151   1328
  Planarity :  0.003   0.049   1376
  Dihedral  : 12.075  74.227   1498
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.07 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 16.92 %
    Favored  : 82.12 %
  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:  1.52 (0.28), residues: 965
  helix:  2.33 (0.26), residues: 435
  sheet:  0.13 (0.51), residues: 103
  loop : -0.11 (0.30), residues: 427

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 8429)
  covalent geometry    : angle       0.44000 (11527)
  hydrogen bonds       : bond        0.03610 (  377)
  hydrogen bonds       : angle       3.78863 ( 1045)
  metal coordination   : bond        0.00373 (    4)
  metal coordination   : angle       0.31317 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4174.10 seconds
wall clock time: 71 minutes 34.71 seconds (4294.71 seconds total)