Starting phenix.real_space_refine
on Sun Aug 24 03:02:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pso_17858/08_2025/8pso_17858_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pso_17858/08_2025/8pso_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_17858/08_2025/8pso_17858.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pso_17858/08_2025/8pso_17858.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pso_17858/08_2025/8pso_17858_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pso_17858/08_2025/8pso_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-2.0-5787/lib/python3.9/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: 4.34, per 1000 atoms: 0.27
  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: 1.30
  Conformation dependent library (CDL) restraints added in 500.7 milliseconds
  
  Enol-peptide restraints added in 476.8 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:
      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: 2.51
  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: 3.56

  Time building geometry restraints manager: 1.97 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=" 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=" C6  CTP F   1 "
    ideal  model  delta    sigma   weight residual
    1.390  1.342  0.048 2.00e-02 2.50e+03 5.82e+00
  bond pdb=" C4' CTP F   1 "
       pdb=" O4' CTP F   1 "
    ideal  model  delta    sigma   weight residual
    1.410  1.452 -0.042 2.00e-02 2.50e+03 4.41e+00
  bond pdb=" C4  CTP F   1 "
       pdb=" N3  CTP F   1 "
    ideal  model  delta    sigma   weight residual
    1.380  1.339  0.041 2.00e-02 2.50e+03 4.24e+00
  bond pdb=" C5' CTP F   1 "
       pdb=" O5' CTP F   1 "
    ideal  model  delta    sigma   weight residual
    1.410  1.449 -0.039 2.00e-02 2.50e+03 3.71e+00
  ... (remaining 16365 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.10: 29524
        3.10 -     6.19: 39
        6.19 -     9.29: 3
        9.29 -    12.38: 4
       12.38 -    15.48: 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=" PA  CTP F   1 "
        pdb=" O3A CTP F   1 "
        pdb=" PB  CTP F   1 "
      ideal   model   delta    sigma   weight residual
     120.50  135.98  -15.48 3.00e+00 1.11e-01 2.66e+01
  angle pdb=" C2' CTP F   1 "
        pdb=" C3' CTP F   1 "
        pdb=" C4' CTP F   1 "
      ideal   model   delta    sigma   weight residual
     111.00   99.47   11.53 3.00e+00 1.11e-01 1.48e+01
  angle pdb=" C1' CTP F   1 "
        pdb=" C2' CTP F   1 "
        pdb=" C3' CTP F   1 "
      ideal   model   delta    sigma   weight residual
     111.00   99.93   11.07 3.00e+00 1.11e-01 1.36e+01
  angle pdb=" PB  CTP F   1 "
        pdb=" O3B CTP F   1 "
        pdb=" PG  CTP F   1 "
      ideal   model   delta    sigma   weight residual
     120.50  130.57  -10.07 3.00e+00 1.11e-01 1.13e+01
  ... (remaining 29566 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.72: 7377
       34.72 -    69.44: 317
       69.44 -   104.16: 20
      104.16 -   138.88: 2
      138.88 -   173.61: 2
  Dihedral angle restraints: 7718
    sinusoidal: 4475
      harmonic: 3243
  Sorted by residual:
  dihedral pdb=" O3B CTP F   1 "
           pdb=" O3A CTP F   1 "
           pdb=" PB  CTP F   1 "
           pdb=" PA  CTP F   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     320.71  153.36  167.34     1      2.00e+01 2.50e-03 4.74e+01
  dihedral pdb=" O1G CTP F   1 "
           pdb=" O3B CTP F   1 "
           pdb=" PG  CTP F   1 "
           pdb=" PB  CTP F   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
      82.72  -47.94  130.65     1      2.00e+01 2.50e-03 3.96e+01
  dihedral pdb=" O3A CTP F   1 "
           pdb=" O3B CTP F   1 "
           pdb=" PB  CTP F   1 "
           pdb=" PG  CTP F   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -155.50  -47.76 -107.74     1      2.00e+01 2.50e-03 3.13e+01
  ... (remaining 7715 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1164
       0.050 -    0.100: 129
       0.100 -    0.151: 33
       0.151 -    0.201: 0
       0.201 -    0.251: 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     -2.47   -2.72    0.25 2.00e-01 2.50e+01 1.58e+00
  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
  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    2.56   -0.13 2.00e-01 2.50e+01 4.24e-01
  ... (remaining 1324 not shown)

  Planarity restraints: 2320
  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 2317 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:                  0.000
  Normalize map: mean=0, sd=1:             1.930
  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:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     22.290
  Find NCS groups from input model:        0.090
  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:6.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8773
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   0.122   8437  Z= 0.115
  Angle     :  0.562  15.480  11535  Z= 0.274
  Chirality :  0.036   0.251   1327
  Planarity :  0.005   0.082   1377
  Dihedral  : 18.686 173.606   3344
  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 aren 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
  covalent geometry    : bond        0.00267 ( 8433)
  covalent geometry    : angle       0.56206 (11533)
  hydrogen bonds       : bond        0.12060 (  389)
  hydrogen bonds       : angle       4.95017 ( 1060)
  metal coordination   : bond        0.00502 (    4)
  metal coordination   : angle       0.60854 (    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  : 0.359 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 9
  residues processed: 126
  average time/residue: 1.4617
  time to fit residues: 193.0210
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  : 0.288 
-------------------------------------------------------------------------------
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:    6.9990
   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:    2.9990
   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:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3294 r_free = 0.3294 target = 0.117993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.092003 restraints weight = 22507.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.2922 rms_B_bonded: 1.30
r_work: 0.2810 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2701 rms_B_bonded: 2.63 restraints_weight: 0.2500
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2691
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2691 r_free = 0.2691    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2691 r_free = 0.2691    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2691
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8822
moved from start:          0.0704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   8437  Z= 0.221
  Angle     :  0.614   8.857  11535  Z= 0.323
  Chirality :  0.041   0.178   1327
  Planarity :  0.005   0.045   1377
  Dihedral  : 14.126 166.605   1505
  Min Nonbonded Distance : 1.772

Molprobity Statistics.
  All-atom Clashscore : 1.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 18.24 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.26), residues: 965
  helix:  1.76 (0.25), residues: 427
  sheet:  0.66 (0.51), residues: 93
  loop : -0.14 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 206 
 TYR   0.014   0.002   TYR A 403 
 PHE   0.019   0.002   PHE C  44 
 TRP   0.008   0.002   TRP B 432 
 HIS   0.008   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 8433)
  covalent geometry    : angle       0.61355 (11533)
  hydrogen bonds       : bond        0.05966 (  389)
  hydrogen bonds       : angle       4.38931 ( 1060)
  metal coordination   : bond        0.01077 (    4)
  metal coordination   : angle       0.24249 (    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: 16
    poor density    : 115
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  332 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8333 (ttp80)
  outliers start: 16
  outliers final: 9
  residues processed: 126
  average time/residue: 1.4324
  time to fit residues: 189.0721
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  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 SER
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
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:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3319 r_free = 0.3319 target = 0.119866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.093885 restraints weight = 22853.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.2956 rms_B_bonded: 1.28
r_work: 0.2845 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.2737 rms_B_bonded: 2.67 restraints_weight: 0.2500
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2730
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2730 r_free = 0.2730    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2730 r_free = 0.2730    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2730
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8792
moved from start:          0.0668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8437  Z= 0.128
  Angle     :  0.528   7.558  11535  Z= 0.276
  Chirality :  0.037   0.145   1327
  Planarity :  0.004   0.048   1377
  Dihedral  : 13.507 165.309   1499
  Min Nonbonded Distance : 1.831

Molprobity Statistics.
  All-atom Clashscore : 1.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 18.59 %
    Favored  : 79.98 %
  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:  1.21 (0.27), residues: 965
  helix:  1.86 (0.25), residues: 429
  sheet:  0.58 (0.51), residues: 95
  loop : -0.15 (0.29), residues: 441

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   0.013   0.001   PHE C  44 
 TRP   0.005   0.001   TRP A 346 
 HIS   0.005   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 8433)
  covalent geometry    : angle       0.52808 (11533)
  hydrogen bonds       : bond        0.04859 (  389)
  hydrogen bonds       : angle       4.20672 ( 1060)
  metal coordination   : bond        0.00841 (    4)
  metal coordination   : angle       0.29640 (    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: 12
    poor density    : 117
  time to evaluate  : 0.344 
Fit side-chains
REVERT: C  100 ASP cc_start: 0.7377 (t0) cc_final: 0.7175 (t0)
  outliers start: 12
  outliers final: 5
  residues processed: 126
  average time/residue: 1.7223
  time to fit residues: 227.3678
Evaluate side-chains
  117 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 112
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0870
   chunk 66 optimal weight:    0.1980
   chunk 40 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0980
   chunk 90 optimal weight:    0.0570
   chunk 9 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.2876

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3361 r_free = 0.3361 target = 0.123073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.097390 restraints weight = 22696.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.2992 rms_B_bonded: 1.28
r_work: 0.2884 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2778 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2790
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2790
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8746
moved from start:          0.0717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8437  Z= 0.090
  Angle     :  0.478   6.107  11535  Z= 0.248
  Chirality :  0.036   0.142   1327
  Planarity :  0.004   0.052   1377
  Dihedral  : 13.052 164.313   1498
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 1.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 18.36 %
    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 aren not related in a simple way.
  whole:  1.44 (0.27), residues: 965
  helix:  2.10 (0.25), residues: 429
  sheet:  0.64 (0.52), residues: 95
  loop : -0.07 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 475 
 TYR   0.010   0.001   TYR A 403 
 PHE   0.008   0.001   PHE C  44 
 TRP   0.003   0.001   TRP B 432 
 HIS   0.003   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00198 ( 8433)
  covalent geometry    : angle       0.47757 (11533)
  hydrogen bonds       : bond        0.03875 (  389)
  hydrogen bonds       : angle       3.98737 ( 1060)
  metal coordination   : bond        0.00639 (    4)
  metal coordination   : angle       0.57447 (    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
  116 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 109
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
REVERT: A  332 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8256 (ttp80)
REVERT: C  100 ASP cc_start: 0.7453 (t0) cc_final: 0.7208 (t0)
  outliers start: 7
  outliers final: 4
  residues processed: 114
  average time/residue: 1.7804
  time to fit residues: 211.8825
Evaluate side-chains
  111 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 106
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 C residue   17 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 81 optimal weight:    2.9990
   chunk 72 optimal weight:    0.2980
   chunk 69 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3332 r_free = 0.3332 target = 0.120872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.094901 restraints weight = 22640.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 1.28
r_work: 0.2859 rms_B_bonded: 1.62 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: 0.2752
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2752 r_free = 0.2752    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2752 r_free = 0.2752    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2752
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8776
moved from start:          0.0783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8437  Z= 0.120
  Angle     :  0.505   6.894  11535  Z= 0.263
  Chirality :  0.037   0.145   1327
  Planarity :  0.004   0.051   1377
  Dihedral  : 13.143 164.301   1497
  Min Nonbonded Distance : 1.817

Molprobity Statistics.
  All-atom Clashscore : 1.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 17.76 %
    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 aren not related in a simple way.
  whole:  1.40 (0.27), residues: 965
  helix:  2.04 (0.25), residues: 429
  sheet:  0.79 (0.52), residues: 93
  loop : -0.10 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 475 
 TYR   0.012   0.001   TYR A 403 
 PHE   0.013   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        0.00267 ( 8433)
  covalent geometry    : angle       0.50535 (11533)
  hydrogen bonds       : bond        0.04469 (  389)
  hydrogen bonds       : angle       4.03372 ( 1060)
  metal coordination   : bond        0.00770 (    4)
  metal coordination   : angle       0.09591 (    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: 12
    poor density    : 108
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
REVERT: A  332 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8272 (ttp80)
REVERT: C  100 ASP cc_start: 0.7479 (t0) cc_final: 0.7191 (t0)
  outliers start: 12
  outliers final: 5
  residues processed: 117
  average time/residue: 1.8622
  time to fit residues: 227.3765
Evaluate side-chains
  117 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue  371 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   80 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 3 optimal weight:    0.4980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 155 GLN
B 201 GLN
B 211 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.120015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.094102 restraints weight = 22559.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.2956 rms_B_bonded: 1.29
r_work: 0.2847 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 2.64 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2730
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2730 r_free = 0.2730    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2730 r_free = 0.2730    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2730
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8791
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      :  0.003   0.026   8437  Z= 0.138
  Angle     :  0.530   7.793  11535  Z= 0.277
  Chirality :  0.037   0.147   1327
  Planarity :  0.004   0.074   1377
  Dihedral  : 13.378 164.148   1497
  Min Nonbonded Distance : 1.805

Molprobity Statistics.
  All-atom Clashscore : 1.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 17.52 %
    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 aren not related in a simple way.
  whole:  1.30 (0.27), residues: 965
  helix:  1.95 (0.25), residues: 429
  sheet:  0.62 (0.51), residues: 95
  loop : -0.12 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 475 
 TYR   0.012   0.001   TYR A 403 
 PHE   0.015   0.002   PHE C  44 
 TRP   0.006   0.001   TRP A 346 
 HIS   0.004   0.001   HIS B 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8433)
  covalent geometry    : angle       0.53036 (11533)
  hydrogen bonds       : bond        0.04838 (  389)
  hydrogen bonds       : angle       4.10320 ( 1060)
  metal coordination   : bond        0.00789 (    4)
  metal coordination   : angle       0.07594 (    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
  125 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A  332 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8318 (ttp80)
REVERT: C  100 ASP cc_start: 0.7481 (t0) cc_final: 0.7173 (t0)
  outliers start: 13
  outliers final: 5
  residues processed: 120
  average time/residue: 1.6704
  time to fit residues: 209.4960
Evaluate side-chains
  120 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 114
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue  371 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 56 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 87 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0870
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.121423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.095529 restraints weight = 22572.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 1.27
r_work: 0.2870 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2764 rms_B_bonded: 2.65 restraints_weight: 0.2500
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2749
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2749 r_free = 0.2749    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2749 r_free = 0.2749    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2749
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8771
moved from start:          0.0870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8437  Z= 0.108
  Angle     :  0.498   6.772  11535  Z= 0.260
  Chirality :  0.036   0.143   1327
  Planarity :  0.004   0.066   1377
  Dihedral  : 13.217 163.641   1497
  Min Nonbonded Distance : 1.840

Molprobity Statistics.
  All-atom Clashscore : 1.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 18.36 %
    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 aren not related in a simple way.
  whole:  1.38 (0.27), residues: 965
  helix:  2.03 (0.25), residues: 429
  sheet:  0.76 (0.52), residues: 93
  loop : -0.11 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 475 
 TYR   0.011   0.001   TYR A 403 
 PHE   0.011   0.001   PHE C  44 
 TRP   0.004   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 8433)
  covalent geometry    : angle       0.49822 (11533)
  hydrogen bonds       : bond        0.04308 (  389)
  hydrogen bonds       : angle       4.01556 ( 1060)
  metal coordination   : bond        0.00672 (    4)
  metal coordination   : angle       0.36658 (    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
  123 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
REVERT: A  332 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8285 (ttp80)
REVERT: B  486 ILE cc_start: 0.7264 (OUTLIER) cc_final: 0.7034 (mt)
REVERT: C  100 ASP cc_start: 0.7531 (t0) cc_final: 0.7172 (t0)
  outliers start: 10
  outliers final: 5
  residues processed: 121
  average time/residue: 1.6124
  time to fit residues: 204.0296
Evaluate side-chains
  118 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 111
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain B residue  486 ILE
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:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 66 optimal weight:    0.5980
   chunk 72 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0670
   chunk 50 optimal weight:    1.9990
   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:    0.8722

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3328 r_free = 0.3328 target = 0.120600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.094631 restraints weight = 22501.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.2961 rms_B_bonded: 1.27
r_work: 0.2850 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2743 rms_B_bonded: 2.65 restraints_weight: 0.2500
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2734
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2734 r_free = 0.2734    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2734 r_free = 0.2734    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2734
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8783
moved from start:          0.0883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8437  Z= 0.124
  Angle     :  0.512   7.240  11535  Z= 0.267
  Chirality :  0.037   0.145   1327
  Planarity :  0.004   0.052   1377
  Dihedral  : 13.308 163.763   1497
  Min Nonbonded Distance : 1.816

Molprobity Statistics.
  All-atom Clashscore : 1.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 18.24 %
    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 aren not related in a simple way.
  whole:  1.32 (0.27), residues: 965
  helix:  1.97 (0.25), residues: 429
  sheet:  0.70 (0.52), residues: 93
  loop : -0.13 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   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 B 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 8433)
  covalent geometry    : angle       0.51196 (11533)
  hydrogen bonds       : bond        0.04588 (  389)
  hydrogen bonds       : angle       4.04817 ( 1060)
  metal coordination   : bond        0.00752 (    4)
  metal coordination   : angle       0.27005 (    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
  126 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
REVERT: A  332 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8299 (ttp80)
REVERT: B  486 ILE cc_start: 0.7266 (OUTLIER) cc_final: 0.7021 (mt)
REVERT: C  100 ASP cc_start: 0.7544 (t0) cc_final: 0.7174 (t0)
  outliers start: 13
  outliers final: 6
  residues processed: 123
  average time/residue: 1.6071
  time to fit residues: 206.9639
Evaluate side-chains
  117 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  453 SER
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain B residue  486 ILE
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   80 LEU
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:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 65 optimal weight:    0.4980
   chunk 95 optimal weight:    1.9990
   overall best weight:    1.4988

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3301 r_free = 0.3301 target = 0.118492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.092242 restraints weight = 22452.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.2928 rms_B_bonded: 1.31
r_work: 0.2816 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2707 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2696
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2696 r_free = 0.2696    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2696 r_free = 0.2696    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2696
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8805
moved from start:          0.0975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8437  Z= 0.177
  Angle     :  0.571   8.869  11535  Z= 0.299
  Chirality :  0.039   0.162   1327
  Planarity :  0.004   0.055   1377
  Dihedral  : 13.611 163.932   1497
  Min Nonbonded Distance : 1.797

Molprobity Statistics.
  All-atom Clashscore : 1.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 18.24 %
    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 aren not related in a simple way.
  whole:  1.10 (0.26), residues: 965
  helix:  1.76 (0.25), residues: 428
  sheet:  0.62 (0.50), residues: 93
  loop : -0.22 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 475 
 TYR   0.013   0.001   TYR A 403 
 PHE   0.018   0.002   PHE C  44 
 TRP   0.007   0.001   TRP A 346 
 HIS   0.006   0.001   HIS B 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 8433)
  covalent geometry    : angle       0.57102 (11533)
  hydrogen bonds       : bond        0.05425 (  389)
  hydrogen bonds       : angle       4.21858 ( 1060)
  metal coordination   : bond        0.00916 (    4)
  metal coordination   : angle       0.37291 (    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
  119 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
REVERT: A  332 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8345 (ttp80)
REVERT: C  100 ASP cc_start: 0.7538 (t0) cc_final: 0.7191 (t0)
  outliers start: 10
  outliers final: 5
  residues processed: 116
  average time/residue: 1.6679
  time to fit residues: 202.0778
Evaluate side-chains
  114 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue  371 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:    4.9990
   chunk 95 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B 201 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.119823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.093874 restraints weight = 22535.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 1.27
r_work: 0.2844 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2737 rms_B_bonded: 2.64 restraints_weight: 0.2500
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2727
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2727 r_free = 0.2727    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 = 0.2727 r_free = 0.2727    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2727
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8794
moved from start:          0.0951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8437  Z= 0.135
  Angle     :  0.530   7.572  11535  Z= 0.278
  Chirality :  0.037   0.145   1327
  Planarity :  0.004   0.062   1377
  Dihedral  : 13.454 163.424   1497
  Min Nonbonded Distance : 1.816

Molprobity Statistics.
  All-atom Clashscore : 1.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 18.59 %
    Favored  : 80.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.27), residues: 965
  helix:  1.82 (0.25), residues: 429
  sheet:  0.52 (0.51), residues: 95
  loop : -0.19 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 475 
 TYR   0.012   0.001   TYR A 403 
 PHE   0.014   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
  covalent geometry    : bond        0.00301 ( 8433)
  covalent geometry    : angle       0.52985 (11533)
  hydrogen bonds       : bond        0.04861 (  389)
  hydrogen bonds       : angle       4.15425 ( 1060)
  metal coordination   : bond        0.00713 (    4)
  metal coordination   : angle       0.23546 (    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
  117 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
REVERT: A  332 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8330 (ttp80)
REVERT: C  100 ASP cc_start: 0.7550 (t0) cc_final: 0.7183 (t0)
  outliers start: 9
  outliers final: 6
  residues processed: 117
  average time/residue: 1.6998
  time to fit residues: 207.9157
Evaluate side-chains
  115 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 108
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue  211 ASN
Chi-restraints excluded: chain B residue  219 GLU
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  453 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 16 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9990
   chunk 89 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 93 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
B 201 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.120462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.094518 restraints weight = 22484.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.2955 rms_B_bonded: 1.28
r_work: 0.2846 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 2.64 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2738
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2738 r_free = 0.2738    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 = 0.2738 r_free = 0.2738    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2738
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8784
moved from start:          0.0941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8437  Z= 0.117
  Angle     :  0.515   7.193  11535  Z= 0.269
  Chirality :  0.037   0.143   1327
  Planarity :  0.004   0.061   1377
  Dihedral  : 13.375 163.381   1497
  Min Nonbonded Distance : 1.833

Molprobity Statistics.
  All-atom Clashscore : 1.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 18.47 %
    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 aren not related in a simple way.
  whole:  1.24 (0.27), residues: 965
  helix:  1.89 (0.25), residues: 429
  sheet:  0.64 (0.52), residues: 93
  loop : -0.17 (0.29), residues: 443

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   0.013   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
  covalent geometry    : bond        0.00258 ( 8433)
  covalent geometry    : angle       0.51544 (11533)
  hydrogen bonds       : bond        0.04599 (  389)
  hydrogen bonds       : angle       4.10125 ( 1060)
  metal coordination   : bond        0.00668 (    4)
  metal coordination   : angle       0.28265 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6635.24 seconds
wall clock time: 112 minutes 56.48 seconds (6776.48 seconds total)