Starting phenix.real_space_refine
on Fri Jul  3 22:03:21 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pso_17858/07_2026/8pso_17858_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pso_17858/07_2026/8pso_17858.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pso_17858/07_2026/8pso_17858.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pso_17858/07_2026/8pso_17858.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pso_17858/07_2026/8pso_17858_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pso_17858/07_2026/8pso_17858_trim.cif"
  }
  resolution = 2.4
  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=   0.004
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: 8
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      31      5.49       5
     Mg      2      5.21       5
     S      44      5.16       5
     C    5046      2.51       5
     N    1459      2.21       5
     O    1681      1.98       5
     H    7937      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 16201
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 5036
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 5036
          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: 406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 406
          Classifications: {'RNA': 13}
          Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 7}
          Link IDs: {'rna2p': 4, 'rna3p': 8}
    Chain: "S"
      Number of atoms: 476
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 476
          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: "F"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'CTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Classifications: {'water': 10}
          Link IDs: {None: 9}
    Chain: "B"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 27
          Classifications: {'water': 27}
          Link IDs: {None: 26}
    Chain: "V"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "S"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "F"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    969  SG  CYS A 161      47.014  44.089  83.490  1.00 27.60           S
  ATOM   2857  SG  CYS A 282      45.317  46.416  86.158  1.00 26.75           S

  Time building chain proxies: 4.01, per 1000 atoms: 0.25
  Number of scatterers: 16201
  At special positions: 0
  Unit cell: (88.2, 94.92, 102.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     Zn      1     29.99
     S      44     16.00
     P      31     15.00
     Mg      2     11.99
     O    1681      8.00
     N    1459      7.00
     C    5046      6.00
     H    7937      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: 1.45
  Conformation dependent library (CDL) restraints added in 492.0 milliseconds
  
  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:
      41 helices and 10 sheets defined
      48.1% alpha, 12.8% beta
      7 base pairs and 7 stacking pairs defined.
    Time for finding SS restraints: 2.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 112 through 123
    Processing helix  chain 'A' and resid 141 through 157
      removed outlier: 3.657A  pdb=" N   ILE A 145 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 169
      removed outlier: 3.540A  pdb=" N   GLY A 168 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 189
    Processing helix  chain 'A' and resid 223 through 236
      removed outlier: 3.585A  pdb=" N   THR A 235 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 4.130A  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: 3.626A  pdb=" N   LEU A 322 " --> pdb=" O   GLU A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 356
      removed outlier: 3.511A  pdb=" N   VAL A 348 " --> pdb=" O   THR A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 374
      removed outlier: 3.930A  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
    Processing helix  chain 'A' and resid 394 through 415
    Processing helix  chain 'B' and resid 1 through 5
      removed outlier: 3.579A  pdb=" N   GLN B   5 " --> pdb=" O   TRP B   2 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 40
      removed outlier: 3.563A  pdb=" N   GLY B  40 " --> pdb=" O   GLU B  36 " (cutoff:3.500A)
    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 204
    Processing helix  chain 'B' and resid 217 through 221
    Processing helix  chain 'B' and resid 222 through 234
    Processing helix  chain 'B' and resid 235 through 248
      removed outlier: 3.737A  pdb=" N   GLY B 239 " --> pdb=" O   MET B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 279
      removed outlier: 3.809A  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
    Processing helix  chain 'B' and resid 419 through 425
    Processing helix  chain 'B' and resid 429 through 436
      removed outlier: 3.979A  pdb=" N   GLN B 434 " --> pdb=" O   PHE B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 454
    Processing helix  chain 'B' and resid 479 through 496
    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: 3.677A  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: 3.687A  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
    Processing helix  chain 'C' and resid 100 through 107
    Processing sheet with id=AA1, first strand: chain 'A' and resid 136 through 137
    Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 194
      removed outlier: 6.234A  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: 6.234A  pdb=" N   TRP A 198 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   SER A 248 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   LEU A 277 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      removed outlier: 4.259A  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: 3.726A  pdb=" N   ARG B 155 " --> pdb=" O   ARG B 145 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   PHE B 140 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 285 through 287
    Processing sheet with id=AA8, first strand: chain 'B' and resid 326 through 329
    Processing sheet with id=AA9, first strand: chain 'B' and resid 477 through 478
    Processing sheet with id=AB1, first strand: chain 'C' and resid 72 through 83
      removed outlier: 7.242A  pdb=" N   LYS C  75 " --> pdb=" O   TYR C 119 " (cutoff:3.500A)
      removed outlier: 5.391A  pdb=" N   TYR C 119 " --> pdb=" O   LYS C  75 " (cutoff:3.500A)

    379 hydrogen bonds defined for protein.
    1026 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      17 hydrogen bonds
      34 hydrogen bond angles
      0 basepair planarities
      7 basepair parallelities
      7 stacking parallelities
  Total time for adding SS restraints: 3.34

  Time building geometry restraints manager: 2.01 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: 7915
        1.03 -     1.23: 32
        1.23 -     1.42: 3521
        1.42 -     1.61: 4838
        1.61 -     1.81: 64
  Bond restraints: 16370
  Sorted by residual:
  bond pdb=" O3B CTP F   1 "
       pdb=" PG  CTP F   1 "
    ideal  model  delta    sigma   weight residual
    1.751  1.613  0.138 2.00e-02 2.50e+03 4.73e+01
  bond pdb=" O3A CTP F   1 "
       pdb=" PB  CTP F   1 "
    ideal  model  delta    sigma   weight residual
    1.675  1.602  0.073 2.00e-02 2.50e+03 1.35e+01
  bond pdb=" O5' CTP F   1 "
       pdb=" PA  CTP F   1 "
    ideal  model  delta    sigma   weight residual
    1.660  1.603  0.057 2.00e-02 2.50e+03 8.05e+00
  bond pdb=" CB  PRO B 470 "
       pdb=" CG  PRO B 470 "
    ideal  model  delta    sigma   weight residual
    1.492  1.614 -0.122 5.00e-02 4.00e+02 5.94e+00
  bond pdb=" C5' CTP F   1 "
       pdb=" O5' CTP F   1 "
    ideal  model  delta    sigma   weight residual
    1.405  1.449 -0.044 2.00e-02 2.50e+03 4.73e+00
  ... (remaining 16365 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 29275
        1.79 -     3.58: 276
        3.58 -     5.37: 16
        5.37 -     7.16: 3
        7.16 -     8.94: 1
  Bond angle restraints: 29571
  Sorted by residual:
  angle pdb=" CA  PRO B 470 "
        pdb=" N   PRO B 470 "
        pdb=" CD  PRO B 470 "
      ideal   model   delta    sigma   weight residual
     112.00  103.06    8.94 1.40e+00 5.10e-01 4.08e+01
  angle pdb=" N   PRO B 470 "
        pdb=" CD  PRO B 470 "
        pdb=" CG  PRO B 470 "
      ideal   model   delta    sigma   weight residual
     103.20   98.90    4.30 1.50e+00 4.44e-01 8.22e+00
  angle pdb=" CA  GLU C  89 "
        pdb=" CB  GLU C  89 "
        pdb=" CG  GLU C  89 "
      ideal   model   delta    sigma   weight residual
     114.10  118.95   -4.85 2.00e+00 2.50e-01 5.87e+00
  angle pdb=" N   PRO B 470 "
        pdb=" CA  PRO B 470 "
        pdb=" CB  PRO B 470 "
      ideal   model   delta    sigma   weight residual
     103.25  100.80    2.45 1.05e+00 9.07e-01 5.45e+00
  angle pdb=" C2' CTP F   1 "
        pdb=" C3' CTP F   1 "
        pdb=" O3' CTP F   1 "
      ideal   model   delta    sigma   weight residual
     108.05  114.30   -6.25 3.00e+00 1.11e-01 4.34e+00
  ... (remaining 29566 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.72: 7393
       34.72 -    69.44: 321
       69.44 -   104.16: 27
      104.16 -   138.88: 0
      138.88 -   173.61: 1
  Dihedral angle restraints: 7742
    sinusoidal: 4499
      harmonic: 3243
  Sorted by residual:
  dihedral pdb=" C4'   G S   1 "
           pdb=" C3'   G S   1 "
           pdb=" O3'   G S   1 "
           pdb=" P     U S   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -110.00   63.61 -173.61     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" CA  LEU B 265 "
           pdb=" C   LEU B 265 "
           pdb=" N   MET B 266 "
           pdb=" CA  MET B 266 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.25   19.75     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CB  GLU A 287 "
           pdb=" CG  GLU A 287 "
           pdb=" CD  GLU A 287 "
           pdb=" OE1 GLU A 287 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.78   89.78     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 7739 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1086
       0.041 -    0.081: 174
       0.081 -    0.122: 59
       0.122 -    0.163: 7
       0.163 -    0.203: 1
  Chirality restraints: 1327
  Sorted by residual:
  chirality pdb=" C2' CTP F   1 "
            pdb=" C1' CTP F   1 "
            pdb=" C3' CTP F   1 "
            pdb=" O2' CTP F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52   -2.72    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" C1' CTP F   1 "
            pdb=" C2' CTP F   1 "
            pdb=" N1  CTP F   1 "
            pdb=" O4' CTP F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.50   -0.15 2.00e-01 2.50e+01 5.28e-01
  chirality pdb=" C3'   G S   1 "
            pdb=" C4'   G S   1 "
            pdb=" O3'   G S   1 "
            pdb=" C2'   G S   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.60   -0.14 2.00e-01 2.50e+01 5.14e-01
  ... (remaining 1324 not shown)

  Planarity restraints: 2319
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 469 "   -0.057 5.00e-02 4.00e+02   8.16e-02 1.07e+01
        pdb=" N   PRO B 470 "    0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO B 470 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B 470 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 161 "   -0.029 5.00e-02 4.00e+02   4.38e-02 3.07e+00
        pdb=" N   PRO B 162 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO B 162 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 162 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A S   8 "   -0.022 2.00e-02 2.50e+03   9.61e-03 3.00e+00
        pdb=" N9    A S   8 "    0.026 2.00e-02 2.50e+03
        pdb=" C8    A S   8 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A S   8 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    A S   8 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A S   8 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6    A S   8 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1    A S   8 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A S   8 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    A S   8 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    A S   8 "    0.001 2.00e-02 2.50e+03
        pdb=" H8    A S   8 "    0.001 2.00e-02 2.50e+03
        pdb=" H2    A S   8 "    0.001 2.00e-02 2.50e+03
  ... (remaining 2316 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.15: 537
        2.15 -     2.76: 29691
        2.76 -     3.37: 46745
        3.37 -     3.99: 62048
        3.99 -     4.60: 95312
  Nonbonded interactions: 234333
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU C  89 "
            pdb=" H   GLU C  89 "
     model   vdw
     1.532 2.450
  nonbonded pdb=" OD2 ASP B 222 "
            pdb="HH22 ARG B 247 "
     model   vdw
     1.614 2.450
  nonbonded pdb=" OD1 ASP B 444 "
            pdb=" H   ASP B 444 "
     model   vdw
     1.628 2.450
  nonbonded pdb=" HZ3 LYS B 249 "
            pdb=" O   CYS B 260 "
     model   vdw
     1.637 2.450
  nonbonded pdb=" HH  TYR B 186 "
            pdb=" O   SER B 286 "
     model   vdw
     1.639 2.450
  ... (remaining 234328 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:                  0.010
  Normalize map: mean=0, sd=1:             1.750
  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:             0.110
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     23.080
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8841
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   0.138   8437  Z= 0.144
  Angle     :  0.505   8.944  11535  Z= 0.274
  Chirality :  0.036   0.203   1327
  Planarity :  0.005   0.082   1376
  Dihedral  : 18.700 173.606   3368
  Min Nonbonded Distance : 1.693

Molprobity Statistics.
  All-atom Clashscore : 2.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 19.90 %
    Favored  : 78.55 %
  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 are not related in a simple way.
  whole:  1.47 (0.27), residues: 965
  helix:  2.12 (0.25), residues: 421
  sheet:  0.72 (0.52), residues: 93
  loop : -0.03 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 206 
 TYR   0.008   0.001   TYR A 403 
 PHE   0.009   0.001   PHE C  44 
 TRP   0.004   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A 296 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.14 ( 8433)
  covalent geometry    : angle       0.50547 /  0.27 (11533)
  hydrogen bonds       : bond        0.12060 /  8.81 (  389)
  hydrogen bonds       : angle       4.95017 /  3.60 ( 1060)
  metal coordination   : bond        0.00502 /  0.36 (    4)
  metal coordination   : angle       0.60854 /  0.21 (    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
  129 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 9
  residues processed: 126
  average time/residue: 1.4197
  time to fit residues: 188.4592
Evaluate side-chains
  123 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 114
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   30 SER
Chi-restraints excluded: chain C residue   67 SER
Chi-restraints excluded: chain C residue   87 THR
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:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    1.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 201 GLN
B 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.119164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.093201 restraints weight = 22517.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.2938 rms_B_bonded: 1.30
r_work: 0.2826 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2717 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2718
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2718
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8881
moved from start:          0.0524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   8437  Z= 0.188
  Angle     :  0.557   5.248  11535  Z= 0.302
  Chirality :  0.039   0.152   1327
  Planarity :  0.005   0.044   1376
  Dihedral  : 14.323 167.510   1529
  Min Nonbonded Distance : 1.739

Molprobity Statistics.
  All-atom Clashscore : 1.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 18.12 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.27), residues: 965
  helix:  1.91 (0.25), residues: 428
  sheet:  0.61 (0.52), residues: 93
  loop : -0.10 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 206 
 TYR   0.014   0.002   TYR A 403 
 PHE   0.018   0.002   PHE C  44 
 TRP   0.007   0.001   TRP B 432 
 HIS   0.007   0.001   HIS A 367 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00422 /  0.19 ( 8433)
  covalent geometry    : angle       0.55669 /  0.30 (11533)
  hydrogen bonds       : bond        0.05541 /  3.93 (  389)
  hydrogen bonds       : angle       4.34738 /  3.14 ( 1060)
  metal coordination   : bond        0.00959 /  0.60 (    4)
  metal coordination   : angle       0.15242 /  0.07 (    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
  131 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
REVERT: A  332 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8300 (ttp80)
  outliers start: 15
  outliers final: 10
  residues processed: 127
  average time/residue: 1.5190
  time to fit residues: 203.1035
Evaluate side-chains
  123 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   30 SER
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue   94 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0670
   overall best weight:    0.6518

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 201 GLN
B 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.120988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.095090 restraints weight = 22893.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.2973 rms_B_bonded: 1.29
r_work: 0.2862 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.2754 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2739
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2739 r_free = 0.2739    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2739 r_free = 0.2739    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2739
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8859
moved from start:          0.0528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   8437  Z= 0.110
  Angle     :  0.491   4.743  11535  Z= 0.262
  Chirality :  0.036   0.144   1327
  Planarity :  0.004   0.050   1376
  Dihedral  : 13.863 166.227   1524
  Min Nonbonded Distance : 1.871

Molprobity Statistics.
  All-atom Clashscore : 1.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 18.47 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.27), residues: 965
  helix:  1.97 (0.25), residues: 428
  sheet:  0.64 (0.52), residues: 93
  loop : -0.10 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 475 
 TYR   0.011   0.001   TYR A 403 
 PHE   0.012   0.001   PHE C  44 
 TRP   0.004   0.001   TRP A 346 
 HIS   0.005   0.001   HIS A 367 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00240 /  0.11 ( 8433)
  covalent geometry    : angle       0.49136 /  0.26 (11533)
  hydrogen bonds       : bond        0.04772 /  3.40 (  389)
  hydrogen bonds       : angle       4.22422 /  3.05 ( 1060)
  metal coordination   : bond        0.00669 /  0.46 (    4)
  metal coordination   : angle       0.35153 /  0.13 (    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
  129 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
  outliers start: 11
  outliers final: 8
  residues processed: 127
  average time/residue: 1.3301
  time to fit residues: 178.2098
Evaluate side-chains
  121 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  125 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 66 optimal weight:    0.2980
   chunk 40 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    1.4586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 201 GLN
B 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.118805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.092772 restraints weight = 22696.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.2938 rms_B_bonded: 1.30
r_work: 0.2826 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2718 rms_B_bonded: 2.65 restraints_weight: 0.2500
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2705
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    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 = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2705
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8884
moved from start:          0.0713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8437  Z= 0.173
  Angle     :  0.537   4.801  11535  Z= 0.290
  Chirality :  0.039   0.148   1327
  Planarity :  0.004   0.052   1376
  Dihedral  : 13.962 165.743   1523
  Min Nonbonded Distance : 1.773

Molprobity Statistics.
  All-atom Clashscore : 0.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 17.64 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.27), residues: 965
  helix:  1.81 (0.25), residues: 428
  sheet:  0.53 (0.51), residues: 95
  loop : -0.16 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 475 
 TYR   0.014   0.001   TYR A 403 
 PHE   0.017   0.002   PHE C  44 
 TRP   0.006   0.001   TRP B 432 
 HIS   0.005   0.001   HIS A 367 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00389 /  0.17 ( 8433)
  covalent geometry    : angle       0.53725 /  0.29 (11533)
  hydrogen bonds       : bond        0.05382 /  3.83 (  389)
  hydrogen bonds       : angle       4.24717 /  3.06 ( 1060)
  metal coordination   : bond        0.00957 /  0.59 (    4)
  metal coordination   : angle       0.12242 /  0.06 (    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
  127 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7966 (mmp-170)
  outliers start: 15
  outliers final: 7
  residues processed: 121
  average time/residue: 1.4041
  time to fit residues: 179.0118
Evaluate side-chains
  116 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  189 ARG
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   87 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 42 optimal weight:    0.5980
   chunk 85 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 81 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 201 GLN
B 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.120052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.094117 restraints weight = 22701.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.2950 rms_B_bonded: 1.30
r_work: 0.2841 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2734 rms_B_bonded: 2.64 restraints_weight: 0.2500
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2739
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2739 r_free = 0.2739    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2739 r_free = 0.2739    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (8 function evaluations)
r_final: 0.2739
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8870
moved from start:          0.0766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8437  Z= 0.126
  Angle     :  0.504   4.594  11535  Z= 0.271
  Chirality :  0.037   0.144   1327
  Planarity :  0.004   0.053   1376
  Dihedral  : 13.744 164.920   1523
  Min Nonbonded Distance : 1.835

Molprobity Statistics.
  All-atom Clashscore : 1.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 18.00 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.27), residues: 965
  helix:  1.86 (0.25), residues: 428
  sheet:  0.53 (0.51), residues: 95
  loop : -0.15 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 475 
 TYR   0.012   0.001   TYR A 403 
 PHE   0.014   0.001   PHE C  44 
 TRP   0.005   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.13 ( 8433)
  covalent geometry    : angle       0.50360 /  0.27 (11533)
  hydrogen bonds       : bond        0.04884 /  3.48 (  389)
  hydrogen bonds       : angle       4.19555 /  3.03 ( 1060)
  metal coordination   : bond        0.00788 /  0.52 (    4)
  metal coordination   : angle       0.22933 /  0.09 (    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
  120 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7965 (mmp-170)
REVERT: A  332 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8294 (ttp80)
  outliers start: 10
  outliers final: 6
  residues processed: 119
  average time/residue: 1.4746
  time to fit residues: 184.8133
Evaluate side-chains
  118 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 ARG
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   87 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    1.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 201 GLN
B 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.118541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.092545 restraints weight = 22610.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.2924 rms_B_bonded: 1.30
r_work: 0.2812 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2704 rms_B_bonded: 2.64 restraints_weight: 0.2500
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2699
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2699 r_free = 0.2699    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2699 r_free = 0.2699    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2699
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8890
moved from start:          0.0874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8437  Z= 0.184
  Angle     :  0.549   4.834  11535  Z= 0.297
  Chirality :  0.039   0.149   1327
  Planarity :  0.005   0.057   1376
  Dihedral  : 13.899 164.733   1522
  Min Nonbonded Distance : 1.771

Molprobity Statistics.
  All-atom Clashscore : 1.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 18.00 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.26), residues: 965
  helix:  1.68 (0.25), residues: 428
  sheet:  0.62 (0.51), residues: 93
  loop : -0.26 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 475 
 TYR   0.014   0.002   TYR A 403 
 PHE   0.018   0.002   PHE C  44 
 TRP   0.007   0.001   TRP B 432 
 HIS   0.005   0.001   HIS B 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00414 /  0.18 ( 8433)
  covalent geometry    : angle       0.54939 /  0.30 (11533)
  hydrogen bonds       : bond        0.05544 /  3.94 (  389)
  hydrogen bonds       : angle       4.27118 /  3.08 ( 1060)
  metal coordination   : bond        0.01063 /  0.66 (    4)
  metal coordination   : angle       0.20207 /  0.09 (    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
  122 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7930 (mmp-170)
REVERT: A  332 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8353 (ttp80)
  outliers start: 12
  outliers final: 6
  residues processed: 118
  average time/residue: 1.5208
  time to fit residues: 188.6208
Evaluate side-chains
  119 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 ARG
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   87 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 3 optimal weight:    0.3980
   chunk 56 optimal weight:    0.4980
   chunk 21 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0980
   chunk 34 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 201 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.120607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.094684 restraints weight = 22696.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 1.28
r_work: 0.2856 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2749 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2747
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2747 r_free = 0.2747    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2747 r_free = 0.2747    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2747
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8859
moved from start:          0.0811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8437  Z= 0.104
  Angle     :  0.492   4.860  11535  Z= 0.264
  Chirality :  0.037   0.144   1327
  Planarity :  0.004   0.058   1376
  Dihedral  : 13.457 164.053   1522
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 1.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 17.76 %
    Favored  : 80.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.27), residues: 965
  helix:  1.88 (0.25), residues: 429
  sheet:  0.50 (0.51), residues: 95
  loop : -0.14 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  33 
 TYR   0.010   0.001   TYR A 403 
 PHE   0.012   0.001   PHE C  44 
 TRP   0.005   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00225 /  0.10 ( 8433)
  covalent geometry    : angle       0.49164 /  0.26 (11533)
  hydrogen bonds       : bond        0.04525 /  3.23 (  389)
  hydrogen bonds       : angle       4.16050 /  3.00 ( 1060)
  metal coordination   : bond        0.00659 /  0.46 (    4)
  metal coordination   : angle       0.35756 /  0.12 (    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
  122 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
REVERT: A  332 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8301 (ttp80)
  outliers start: 11
  outliers final: 7
  residues processed: 120
  average time/residue: 1.6062
  time to fit residues: 202.7177
Evaluate side-chains
  121 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  211 ASN
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain C residue   17 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0570
   chunk 66 optimal weight:    0.1980
   chunk 72 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 32 optimal weight:    0.1980
   chunk 50 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.4700

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 201 GLN
B 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.121416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.095541 restraints weight = 22606.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 1.28
r_work: 0.2859 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2753 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2759
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2759
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8850
moved from start:          0.0820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8437  Z= 0.103
  Angle     :  0.486   5.184  11535  Z= 0.260
  Chirality :  0.036   0.142   1327
  Planarity :  0.004   0.077   1376
  Dihedral  : 13.162 164.068   1521
  Min Nonbonded Distance : 1.845

Molprobity Statistics.
  All-atom Clashscore : 1.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 18.12 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.27), residues: 965
  helix:  1.99 (0.25), residues: 429
  sheet:  0.67 (0.52), residues: 93
  loop : -0.13 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 475 
 TYR   0.011   0.001   TYR A 403 
 PHE   0.011   0.001   PHE C  44 
 TRP   0.005   0.001   TRP A 346 
 HIS   0.004   0.001   HIS C  28 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00227 /  0.10 ( 8433)
  covalent geometry    : angle       0.48591 /  0.26 (11533)
  hydrogen bonds       : bond        0.04298 /  3.06 (  389)
  hydrogen bonds       : angle       4.06332 /  2.93 ( 1060)
  metal coordination   : bond        0.00789 /  0.53 (    4)
  metal coordination   : angle       0.56204 /  0.20 (    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
  118 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.436 
Fit side-chains
REVERT: A  332 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8281 (ttp80)
  outliers start: 10
  outliers final: 6
  residues processed: 115
  average time/residue: 1.6225
  time to fit residues: 195.8055
Evaluate side-chains
  114 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue  219 GLU
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   53 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 95 optimal weight:    1.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 201 GLN
B 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.119209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.093234 restraints weight = 22538.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.2935 rms_B_bonded: 1.30
r_work: 0.2823 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 2.64 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2715
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2715 r_free = 0.2715    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2715 r_free = 0.2715    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (5 function evaluations)
r_final: 0.2715
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8881
moved from start:          0.0909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8437  Z= 0.174
  Angle     :  0.540   4.976  11535  Z= 0.290
  Chirality :  0.038   0.147   1327
  Planarity :  0.005   0.068   1376
  Dihedral  : 13.436 164.341   1521
  Min Nonbonded Distance : 1.772

Molprobity Statistics.
  All-atom Clashscore : 0.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 18.00 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.27), residues: 965
  helix:  1.81 (0.25), residues: 428
  sheet:  0.65 (0.51), residues: 93
  loop : -0.23 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 475 
 TYR   0.014   0.002   TYR A 403 
 PHE   0.017   0.002   PHE C  44 
 TRP   0.006   0.001   TRP A 346 
 HIS   0.005   0.001   HIS B 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00391 /  0.17 ( 8433)
  covalent geometry    : angle       0.53969 /  0.29 (11533)
  hydrogen bonds       : bond        0.05228 /  3.71 (  389)
  hydrogen bonds       : angle       4.17429 /  3.01 ( 1060)
  metal coordination   : bond        0.00947 /  0.59 (    4)
  metal coordination   : angle       0.15546 /  0.07 (    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
  121 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.439 
Fit side-chains
REVERT: A  332 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8348 (ttp80)
  outliers start: 11
  outliers final: 6
  residues processed: 117
  average time/residue: 1.4819
  time to fit residues: 182.1326
Evaluate side-chains
  119 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 112
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue  219 GLU
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain C residue   17 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 201 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.119673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.093702 restraints weight = 22652.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.2956 rms_B_bonded: 1.30
r_work: 0.2846 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2739 rms_B_bonded: 2.65 restraints_weight: 0.2500
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2721
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2721 r_free = 0.2721    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2721 r_free = 0.2721    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2721
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8871
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   0.047   8437  Z= 0.132
  Angle     :  0.517   6.150  11535  Z= 0.278
  Chirality :  0.037   0.146   1327
  Planarity :  0.004   0.064   1376
  Dihedral  : 13.396 164.024   1521
  Min Nonbonded Distance : 1.813

Molprobity Statistics.
  All-atom Clashscore : 1.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 18.36 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.27), residues: 965
  helix:  1.83 (0.25), residues: 428
  sheet:  0.51 (0.51), residues: 95
  loop : -0.18 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 475 
 TYR   0.012   0.001   TYR A 403 
 PHE   0.015   0.001   PHE C  44 
 TRP   0.007   0.001   TRP A 346 
 HIS   0.004   0.001   HIS B 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.13 ( 8433)
  covalent geometry    : angle       0.51656 /  0.28 (11533)
  hydrogen bonds       : bond        0.04878 /  3.47 (  389)
  hydrogen bonds       : angle       4.15866 /  3.00 ( 1060)
  metal coordination   : bond        0.00812 /  0.53 (    4)
  metal coordination   : angle       0.11788 /  0.05 (    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
  120 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.410 
Fit side-chains
  outliers start: 9
  outliers final: 8
  residues processed: 118
  average time/residue: 1.4174
  time to fit residues: 176.1986
Evaluate side-chains
  118 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  211 ASN
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  125 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 16 optimal weight:    0.0370
   chunk 20 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9990
   chunk 89 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.6660

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 201 GLN
B 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.120791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.094920 restraints weight = 22595.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 1.27
r_work: 0.2855 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2748 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2736
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2736 r_free = 0.2736    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2736 r_free = 0.2736    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2736
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8858
moved from start:          0.0877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8437  Z= 0.111
  Angle     :  0.497   5.966  11535  Z= 0.266
  Chirality :  0.036   0.144   1327
  Planarity :  0.004   0.063   1376
  Dihedral  : 13.230 163.732   1521
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 0.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 18.59 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.27), residues: 965
  helix:  1.92 (0.25), residues: 429
  sheet:  0.58 (0.51), residues: 93
  loop : -0.16 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 475 
 TYR   0.011   0.001   TYR A 403 
 PHE   0.012   0.001   PHE C  44 
 TRP   0.006   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.11 ( 8433)
  covalent geometry    : angle       0.49683 /  0.27 (11533)
  hydrogen bonds       : bond        0.04502 /  3.20 (  389)
  hydrogen bonds       : angle       4.09144 /  2.95 ( 1060)
  metal coordination   : bond        0.00670 /  0.45 (    4)
  metal coordination   : angle       0.32116 /  0.11 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6331.11 seconds
wall clock time: 107 minutes 47.29 seconds (6467.29 seconds total)