Starting phenix.real_space_refine
on Tue Feb 11 19:52:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pdf_13336/02_2025/7pdf_13336.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pdf_13336/02_2025/7pdf_13336.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pdf_13336/02_2025/7pdf_13336.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pdf_13336/02_2025/7pdf_13336.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pdf_13336/02_2025/7pdf_13336.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pdf_13336/02_2025/7pdf_13336.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 81 atoms to isotropic.
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: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      46      5.16       5
     C    4055      2.51       5
     N    1107      2.21       5
     O    1215      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6427
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 453, 3585
          Classifications: {'peptide': 453}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 9, 'TRANS': 443}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 2809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2809
          Classifications: {'peptide': 341}
          Link IDs: {'PTRANS': 13, 'TRANS': 327}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GSP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.53, per 1000 atoms: 0.70
  Number of scatterers: 6427
  At special positions: 0
  Unit cell: (109.35, 105.3, 102.06, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      46     16.00
     P       3     15.00
     Mg      1     11.99
     O    1215      8.00
     N    1107      7.00
     C    4055      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.85
  Conformation dependent library (CDL) restraints added in 902.7 milliseconds
  

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1494

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 5 sheets defined
      47.6% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 321 through 336
      removed outlier: 4.198A  pdb=" N   VAL A 325 " --> pdb=" O   LYS A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 346
    Processing helix  chain 'A' and resid 354 through 359
    Processing helix  chain 'A' and resid 402 through 407
    Processing helix  chain 'A' and resid 413 through 434
    Processing helix  chain 'A' and resid 457 through 478
    Processing helix  chain 'A' and resid 511 through 523
      removed outlier: 4.120A  pdb=" N   ASN A 515 " --> pdb=" O   SER A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 537
    Processing helix  chain 'A' and resid 1021 through 1037
      removed outlier: 4.073A  pdb=" N   MET A1025 " --> pdb=" O   LYS A1021 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1038 through 1048
      removed outlier: 3.758A  pdb=" N   LYS A1046 " --> pdb=" O   ALA A1042 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   VAL A1047 " --> pdb=" O   GLU A1043 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1079 through 1098
      removed outlier: 3.681A  pdb=" N   TYR A1083 " --> pdb=" O   GLY A1079 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ASP A1092 " --> pdb=" O   GLU A1088 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   PHE A1093 " --> pdb=" O   LEU A1089 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   SER A1098 " --> pdb=" O   ASP A1094 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1131 through 1133
      No H-bonds generated for 'chain 'A' and resid 1131 through 1133'
    Processing helix  chain 'A' and resid 1134 through 1156
    Processing helix  chain 'A' and resid 1190 through 1201
    Processing helix  chain 'A' and resid 1211 through 1219
      removed outlier: 4.089A  pdb=" N   LYS A1219 " --> pdb=" O   ARG A1215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 38
    Processing helix  chain 'B' and resid 52 through 65
    Processing helix  chain 'B' and resid 89 through 110
      removed outlier: 4.031A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 123
      No H-bonds generated for 'chain 'B' and resid 121 through 123'
    Processing helix  chain 'B' and resid 124 through 134
    Processing helix  chain 'B' and resid 143 through 156
      removed outlier: 3.677A  pdb=" N   ASP B 156 " --> pdb=" O   ALA B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 165
      removed outlier: 3.623A  pdb=" N   ARG B 165 " --> pdb=" O   ALA B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 184
      removed outlier: 3.650A  pdb=" N   ASP B 180 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   VAL B 184 " --> pdb=" O   ASP B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 187
      No H-bonds generated for 'chain 'B' and resid 185 through 187'
    Processing helix  chain 'B' and resid 193 through 199
    Processing helix  chain 'B' and resid 233 through 237
    Processing helix  chain 'B' and resid 264 through 278
      removed outlier: 3.534A  pdb=" N   ASN B 278 " --> pdb=" O   LYS B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 304
      removed outlier: 3.563A  pdb=" N   LEU B 297 " --> pdb=" O   LYS B 293 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLY B 304 " --> pdb=" O   LYS B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 312
    Processing helix  chain 'B' and resid 313 through 316
      removed outlier: 3.549A  pdb=" N   ALA B 316 " --> pdb=" O   PRO B 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 313 through 316'
    Processing helix  chain 'B' and resid 331 through 347
    Processing helix  chain 'B' and resid 368 through 388
      removed outlier: 3.854A  pdb=" N   LEU B 388 " --> pdb=" O   GLN B 384 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 439
      removed outlier: 7.265A  pdb=" N   TYR A 446 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   GLN A 389 " --> pdb=" O   CYS A 497 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   CYS A 497 " --> pdb=" O   GLN A 389 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   GLU A 391 " --> pdb=" O   VAL A 495 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   VAL A 495 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439
      removed outlier: 7.265A  pdb=" N   TYR A 446 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   GLN A 389 " --> pdb=" O   CYS A 497 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   CYS A 497 " --> pdb=" O   GLN A 389 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   GLU A 391 " --> pdb=" O   VAL A 495 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   VAL A 495 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
      removed outlier: 8.272A  pdb=" N   HIS A 530 " --> pdb=" O   MET A 486 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   VAL A 488 " --> pdb=" O   HIS A 530 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1052 through 1055
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1106 through 1109
      removed outlier: 7.214A  pdb=" N   MET A1116 " --> pdb=" O   ILE A1108 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   HIS A1170 " --> pdb=" O   SER A1210 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   THR A1240 " --> pdb=" O   GLY A1228 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   GLY A1228 " --> pdb=" O   THR A1240 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   LEU A1242 " --> pdb=" O   TYR A1226 " (cutoff:3.500A)
      removed outlier: 5.496A  pdb=" N   TYR A1226 " --> pdb=" O   LEU A1242 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 208 through 213
      removed outlier: 5.891A  pdb=" N   HIS B  41 " --> pdb=" O   HIS B 220 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   PHE B 222 " --> pdb=" O   HIS B  41 " (cutoff:3.500A)
      removed outlier: 7.158A  pdb=" N   LEU B  43 " --> pdb=" O   PHE B 222 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   ALA B 243 " --> pdb=" O   THR B  40 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ARG B  42 " --> pdb=" O   ALA B 243 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   ILE B 245 " --> pdb=" O   ARG B  42 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   LEU B  44 " --> pdb=" O   ILE B 245 " (cutoff:3.500A)

    309 hydrogen bonds defined for protein.
    891 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.88

  Time building geometry restraints manager: 2.06 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1988
        1.33 -     1.45: 969
        1.45 -     1.57: 3514
        1.57 -     1.69: 5
        1.69 -     1.81: 72
  Bond restraints: 6548
  Sorted by residual:
  bond pdb=" CB  GLU A1088 "
       pdb=" CG  GLU A1088 "
    ideal  model  delta    sigma   weight residual
    1.520  1.472  0.048 3.00e-02 1.11e+03 2.53e+00
  bond pdb=" CB  GLN B  59 "
       pdb=" CG  GLN B  59 "
    ideal  model  delta    sigma   weight residual
    1.520  1.473  0.047 3.00e-02 1.11e+03 2.41e+00
  bond pdb=" CB  TRP A 510 "
       pdb=" CG  TRP A 510 "
    ideal  model  delta    sigma   weight residual
    1.498  1.454  0.044 3.10e-02 1.04e+03 2.05e+00
  bond pdb=" CG1 ILE B 288 "
       pdb=" CD1 ILE B 288 "
    ideal  model  delta    sigma   weight residual
    1.513  1.458  0.055 3.90e-02 6.57e+02 2.02e+00
  bond pdb=" CB  TRP A1188 "
       pdb=" CG  TRP A1188 "
    ideal  model  delta    sigma   weight residual
    1.498  1.457  0.041 3.10e-02 1.04e+03 1.77e+00
  ... (remaining 6543 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 8631
        2.38 -     4.77: 180
        4.77 -     7.15: 16
        7.15 -     9.53: 2
        9.53 -    11.91: 1
  Bond angle restraints: 8830
  Sorted by residual:
  angle pdb=" C   LYS A 437 "
        pdb=" N   ILE A 438 "
        pdb=" CA  ILE A 438 "
      ideal   model   delta    sigma   weight residual
     123.16  118.62    4.54 1.06e+00 8.90e-01 1.83e+01
  angle pdb=" C   TYR A 445 "
        pdb=" N   TYR A 446 "
        pdb=" CA  TYR A 446 "
      ideal   model   delta    sigma   weight residual
     121.75  115.52    6.23 1.73e+00 3.34e-01 1.30e+01
  angle pdb=" N   ILE A1178 "
        pdb=" CA  ILE A1178 "
        pdb=" C   ILE A1178 "
      ideal   model   delta    sigma   weight residual
     110.74  113.98   -3.24 9.10e-01 1.21e+00 1.27e+01
  angle pdb=" CA  LEU A 496 "
        pdb=" CB  LEU A 496 "
        pdb=" CG  LEU A 496 "
      ideal   model   delta    sigma   weight residual
     116.30  128.21  -11.91 3.50e+00 8.16e-02 1.16e+01
  angle pdb=" C1' GSP B 501 "
        pdb=" C2' GSP B 501 "
        pdb=" C3' GSP B 501 "
      ideal   model   delta    sigma   weight residual
     111.00  102.48    8.52 3.00e+00 1.11e-01 8.07e+00
  ... (remaining 8825 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.01: 3469
       17.01 -    34.02: 398
       34.02 -    51.03: 75
       51.03 -    68.05: 10
       68.05 -    85.06: 5
  Dihedral angle restraints: 3957
    sinusoidal: 1643
      harmonic: 2314
  Sorted by residual:
  dihedral pdb=" CA  VAL B 114 "
           pdb=" C   VAL B 114 "
           pdb=" N   PRO B 115 "
           pdb=" CA  PRO B 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.19   29.81     0      5.00e+00 4.00e-02 3.56e+01
  dihedral pdb=" CA  SER A 511 "
           pdb=" C   SER A 511 "
           pdb=" N   ASN A 512 "
           pdb=" CA  ASN A 512 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.98   25.02     0      5.00e+00 4.00e-02 2.50e+01
  dihedral pdb=" CA  VAL A1177 "
           pdb=" C   VAL A1177 "
           pdb=" N   ILE A1178 "
           pdb=" CA  ILE A1178 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.22  -23.78     0      5.00e+00 4.00e-02 2.26e+01
  ... (remaining 3954 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 540
       0.037 -    0.073: 293
       0.073 -    0.110: 102
       0.110 -    0.146: 21
       0.146 -    0.183: 3
  Chirality restraints: 959
  Sorted by residual:
  chirality pdb=" C2' GSP B 501 "
            pdb=" C1' GSP B 501 "
            pdb=" C3' GSP B 501 "
            pdb=" O2' GSP B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.65    0.18 2.00e-01 2.50e+01 8.37e-01
  chirality pdb=" C3' GSP B 501 "
            pdb=" C2' GSP B 501 "
            pdb=" C4' GSP B 501 "
            pdb=" O3' GSP B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.65    0.18 2.00e-01 2.50e+01 8.28e-01
  chirality pdb=" CB  ILE B 235 "
            pdb=" CA  ILE B 235 "
            pdb=" CG1 ILE B 235 "
            pdb=" CG2 ILE B 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.39e-01
  ... (remaining 956 not shown)

  Planarity restraints: 1140
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A1037 "   -0.031 5.00e-02 4.00e+02   4.68e-02 3.51e+00
        pdb=" N   PRO A1038 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A1038 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A1038 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 385 "   -0.006 2.00e-02 2.50e+03   1.19e-02 2.48e+00
        pdb=" CG  PHE A 385 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 385 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 385 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 385 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 385 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 385 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 114 "   -0.024 5.00e-02 4.00e+02   3.63e-02 2.11e+00
        pdb=" N   PRO B 115 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO B 115 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 115 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1137 not shown)

  Histogram of nonbonded interaction distances:
        1.89 -     2.49: 71
        2.49 -     3.09: 5038
        3.09 -     3.69: 10076
        3.69 -     4.30: 14353
        4.30 -     4.90: 23454
  Nonbonded interactions: 52992
  Sorted by model distance:
  nonbonded pdb=" O2G GSP B 501 "
            pdb="MG    MG B 502 "
     model   vdw
     1.885 2.170
  nonbonded pdb=" O2B GSP B 501 "
            pdb="MG    MG B 502 "
     model   vdw
     1.916 2.170
  nonbonded pdb=" O   ALA A 412 "
            pdb=" OG  SER A1052 "
     model   vdw
     2.074 3.040
  nonbonded pdb=" OE2 GLU A1211 "
            pdb=" NH2 ARG A1215 "
     model   vdw
     2.142 3.120
  nonbonded pdb=" O1B GSP B 501 "
            pdb="MG    MG B 502 "
     model   vdw
     2.151 2.170
  ... (remaining 52987 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             1.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     19.010
  Find NCS groups from input model:        0.050
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
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      :  0.008   0.055   6548  Z= 0.529
  Angle     :  0.829  11.913   8830  Z= 0.465
  Chirality :  0.048   0.183    959
  Planarity :  0.004   0.047   1140
  Dihedral  : 14.632  85.056   2463
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 16.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.10 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 12.36 %
    Favored  : 87.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.24 (0.24), residues: 782
  helix: -2.27 (0.21), residues: 368
  sheet: -2.71 (0.40), residues: 121
  loop : -3.38 (0.29), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 277 
 HIS   0.010   0.002   HIS B 220 
 PHE   0.025   0.002   PHE A 385 
 TYR   0.020   0.002   TYR A1083 
 ARG   0.006   0.001   ARG A1026 

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 124
  time to evaluate  : 0.727 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 MET cc_start: 0.8712 (tpp) cc_final: 0.8231 (mmt)
REVERT: A  413 HIS cc_start: 0.8168 (t70) cc_final: 0.7753 (t-90)
REVERT: A 1094 ASP cc_start: 0.8101 (m-30) cc_final: 0.7700 (m-30)
REVERT: A 1106 GLU cc_start: 0.8256 (mp0) cc_final: 0.7773 (mp0)
REVERT: A 1136 LEU cc_start: 0.9520 (mt) cc_final: 0.9212 (mt)
REVERT: A 1157 MET cc_start: 0.8314 (tpp) cc_final: 0.7724 (tpp)
REVERT: B  151 LYS cc_start: 0.7686 (mmpt) cc_final: 0.7471 (mmtt)
  outliers start: 2
  outliers final: 2
  residues processed: 125
  average time/residue: 0.2272
  time to fit residues: 36.2046
Evaluate side-chains
  90 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 88
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  322 ASP
Chi-restraints excluded: chain B residue  114 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 33 optimal weight:    9.9990
   chunk 20 optimal weight:    9.9990
   chunk 40 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0370
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   overall best weight:    0.7260

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

Flipped N/Q/H residues before XYZ refinement:
A 420 ASN
A 458 HIS
A1040 HIS
A1044 GLN
B  41 HIS
B  64 HIS
B  98 ASN
B 124 ASN
B 136 ASN
B 267 GLN
B 271 ASN
B 294 GLN
B 362 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.117856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.093027 restraints weight = 14028.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.095881 restraints weight = 7699.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.097743 restraints weight = 5304.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6548  Z= 0.203
  Angle     :  0.616   8.195   8830  Z= 0.320
  Chirality :  0.043   0.158    959
  Planarity :  0.004   0.055   1140
  Dihedral  :  5.397  48.282    884
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 14.80 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.39 (0.28), residues: 782
  helix: -0.43 (0.26), residues: 377
  sheet: -2.38 (0.41), residues: 123
  loop : -2.70 (0.32), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1159 
 HIS   0.003   0.001   HIS A 530 
 PHE   0.013   0.001   PHE A1142 
 TYR   0.014   0.002   TYR B 163 
 ARG   0.004   0.000   ARG B 389 

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  326 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7235 (tp30)
REVERT: A  333 MET cc_start: 0.8732 (tpp) cc_final: 0.8249 (mmt)
REVERT: A  413 HIS cc_start: 0.8117 (t70) cc_final: 0.7688 (t-90)
REVERT: A  464 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7751 (mt-10)
REVERT: A 1094 ASP cc_start: 0.8162 (m-30) cc_final: 0.7789 (m-30)
REVERT: A 1136 LEU cc_start: 0.9230 (mt) cc_final: 0.8989 (mt)
REVERT: A 1157 MET cc_start: 0.8002 (tpp) cc_final: 0.7227 (tpp)
REVERT: B   59 GLN cc_start: 0.8359 (tp-100) cc_final: 0.7958 (tp40)
REVERT: B  125 GLN cc_start: 0.8150 (tp40) cc_final: 0.7723 (tp-100)
REVERT: B  198 LEU cc_start: 0.9197 (mt) cc_final: 0.8625 (mt)
  outliers start: 13
  outliers final: 4
  residues processed: 137
  average time/residue: 0.1746
  time to fit residues: 32.5567
Evaluate side-chains
  106 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 102
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  379 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 52 optimal weight:    7.9990
   chunk 31 optimal weight:    0.0070
   chunk 64 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 76 optimal weight:    0.5980
   chunk 66 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.6600

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.118912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.094132 restraints weight = 14356.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.097036 restraints weight = 7800.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.098929 restraints weight = 5350.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.2438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6548  Z= 0.188
  Angle     :  0.591   9.030   8830  Z= 0.304
  Chirality :  0.043   0.148    959
  Planarity :  0.003   0.052   1140
  Dihedral  :  5.030  46.657    882
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 19.54 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.29), residues: 782
  helix:  0.22 (0.27), residues: 376
  sheet: -2.04 (0.40), residues: 134
  loop : -2.32 (0.34), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1159 
 HIS   0.003   0.001   HIS B 149 
 PHE   0.014   0.001   PHE B 140 
 TYR   0.016   0.001   TYR B 130 
 ARG   0.003   0.000   ARG B 389 

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 GLU cc_start: 0.8078 (pp20) cc_final: 0.7325 (tm-30)
REVERT: A  326 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7358 (tp30)
REVERT: A  333 MET cc_start: 0.8707 (tpp) cc_final: 0.8309 (mmt)
REVERT: A  413 HIS cc_start: 0.8112 (t70) cc_final: 0.7704 (t-90)
REVERT: A  464 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7802 (mt-10)
REVERT: A 1094 ASP cc_start: 0.8157 (m-30) cc_final: 0.7868 (m-30)
REVERT: A 1136 LEU cc_start: 0.9180 (mt) cc_final: 0.8952 (mt)
REVERT: A 1157 MET cc_start: 0.7864 (tpp) cc_final: 0.7370 (tpp)
REVERT: B  110 MET cc_start: 0.8601 (mtp) cc_final: 0.8273 (mtt)
REVERT: B  125 GLN cc_start: 0.7992 (tp40) cc_final: 0.7517 (tp-100)
  outliers start: 16
  outliers final: 9
  residues processed: 132
  average time/residue: 0.1749
  time to fit residues: 31.9095
Evaluate side-chains
  106 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1138 ILE
Chi-restraints excluded: chain A residue 1151 ASP
Chi-restraints excluded: chain A residue 1183 LEU
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  379 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 14 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0030
   chunk 24 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0870
   overall best weight:    0.5168

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

Flipped N/Q/H residues before XYZ refinement:
A 491 HIS
** B  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.120198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.095631 restraints weight = 14200.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.098496 restraints weight = 7709.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.100399 restraints weight = 5308.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.2821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6548  Z= 0.172
  Angle     :  0.587  10.101   8830  Z= 0.299
  Chirality :  0.042   0.152    959
  Planarity :  0.003   0.052   1140
  Dihedral  :  4.828  46.943    882
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 21.55 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.29), residues: 782
  helix:  0.56 (0.27), residues: 373
  sheet: -1.98 (0.39), residues: 139
  loop : -1.97 (0.34), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1159 
 HIS   0.011   0.001   HIS B 387 
 PHE   0.010   0.001   PHE A1142 
 TYR   0.011   0.001   TYR A1214 
 ARG   0.002   0.000   ARG B 389 

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 GLU cc_start: 0.8023 (pp20) cc_final: 0.7343 (tm-30)
REVERT: A  413 HIS cc_start: 0.8101 (t70) cc_final: 0.7685 (t-90)
REVERT: A  464 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7858 (mt-10)
REVERT: A 1094 ASP cc_start: 0.8146 (m-30) cc_final: 0.7895 (m-30)
REVERT: A 1157 MET cc_start: 0.7649 (tpp) cc_final: 0.7028 (tpp)
REVERT: B  110 MET cc_start: 0.8528 (mtp) cc_final: 0.8256 (mtt)
REVERT: B  125 GLN cc_start: 0.7862 (tp40) cc_final: 0.7425 (pt0)
  outliers start: 13
  outliers final: 6
  residues processed: 119
  average time/residue: 0.1652
  time to fit residues: 27.2659
Evaluate side-chains
  109 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 103
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue 1097 LEU
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain A residue 1183 LEU
Chi-restraints excluded: chain B residue  114 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 27 optimal weight:    0.6980
   chunk 69 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 20 optimal weight:   10.0000
   chunk 66 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 72 optimal weight:    7.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
A1055 HIS
B  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.117216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.092314 restraints weight = 14419.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.095119 restraints weight = 7918.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.096926 restraints weight = 5473.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6548  Z= 0.287
  Angle     :  0.622  10.449   8830  Z= 0.320
  Chirality :  0.044   0.156    959
  Planarity :  0.004   0.052   1140
  Dihedral  :  4.973  47.094    882
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 21.70 %
    Favored  : 75.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.29), residues: 782
  helix:  0.54 (0.27), residues: 377
  sheet: -1.90 (0.40), residues: 136
  loop : -1.96 (0.35), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 281 
 HIS   0.010   0.001   HIS B 387 
 PHE   0.011   0.001   PHE A1168 
 TYR   0.015   0.002   TYR A1083 
 ARG   0.004   0.000   ARG A1215 

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.7497 (p0) cc_final: 0.6179 (p0)
REVERT: A  324 GLU cc_start: 0.8038 (pp20) cc_final: 0.7481 (tm-30)
REVERT: A  464 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7754 (mt-10)
REVERT: A  570 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8569 (mp)
REVERT: A 1094 ASP cc_start: 0.8174 (m-30) cc_final: 0.7884 (m-30)
REVERT: A 1136 LEU cc_start: 0.9282 (mt) cc_final: 0.9038 (mt)
REVERT: A 1157 MET cc_start: 0.7907 (tpp) cc_final: 0.7358 (tpp)
REVERT: A 1241 TYR cc_start: 0.7400 (m-80) cc_final: 0.6928 (m-80)
REVERT: B  110 MET cc_start: 0.8641 (mtp) cc_final: 0.8338 (mtt)
REVERT: B  125 GLN cc_start: 0.7849 (tp40) cc_final: 0.7444 (pt0)
REVERT: B  135 MET cc_start: 0.8449 (ppp) cc_final: 0.8154 (ppp)
  outliers start: 20
  outliers final: 10
  residues processed: 117
  average time/residue: 0.1644
  time to fit residues: 26.6766
Evaluate side-chains
  110 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1138 ILE
Chi-restraints excluded: chain A residue 1183 LEU
Chi-restraints excluded: chain A residue 1232 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  379 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0570
   chunk 23 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9980
   chunk 42 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
A 335 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.119393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.094915 restraints weight = 14178.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.097717 restraints weight = 7778.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.099556 restraints weight = 5390.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.3069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6548  Z= 0.189
  Angle     :  0.603  11.119   8830  Z= 0.305
  Chirality :  0.043   0.273    959
  Planarity :  0.003   0.049   1140
  Dihedral  :  4.809  47.068    882
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 23.56 %
    Favored  : 73.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.29), residues: 782
  helix:  0.66 (0.27), residues: 378
  sheet: -1.77 (0.40), residues: 131
  loop : -1.79 (0.35), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1031 
 HIS   0.011   0.001   HIS B 387 
 PHE   0.011   0.001   PHE A1168 
 TYR   0.017   0.001   TYR A1214 
 ARG   0.003   0.000   ARG A1215 

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.7465 (p0) cc_final: 0.6275 (p0)
REVERT: A  324 GLU cc_start: 0.8071 (pp20) cc_final: 0.7464 (tm-30)
REVERT: A  464 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7830 (mt-10)
REVERT: A 1094 ASP cc_start: 0.8170 (m-30) cc_final: 0.7902 (m-30)
REVERT: A 1157 MET cc_start: 0.7697 (tpp) cc_final: 0.6916 (tpp)
REVERT: A 1241 TYR cc_start: 0.7489 (m-80) cc_final: 0.6874 (m-80)
REVERT: B   92 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8906 (p)
REVERT: B   95 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9301 (mp)
REVERT: B  110 MET cc_start: 0.8619 (mtp) cc_final: 0.8321 (mtt)
REVERT: B  125 GLN cc_start: 0.7804 (tp40) cc_final: 0.7402 (pt0)
REVERT: B  135 MET cc_start: 0.8450 (ppp) cc_final: 0.8142 (ppp)
  outliers start: 19
  outliers final: 9
  residues processed: 124
  average time/residue: 0.1637
  time to fit residues: 28.1927
Evaluate side-chains
  108 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue 1095 GLU
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain A residue 1151 ASP
Chi-restraints excluded: chain A residue 1183 LEU
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  114 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0170
   chunk 69 optimal weight:    0.9980
   chunk 60 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 75 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0770
   chunk 74 optimal weight:    0.3980
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.4576

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.120968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.096793 restraints weight = 14114.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.099569 restraints weight = 7848.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.101436 restraints weight = 5452.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.3316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6548  Z= 0.169
  Angle     :  0.593  11.722   8830  Z= 0.301
  Chirality :  0.042   0.156    959
  Planarity :  0.003   0.047   1140
  Dihedral  :  4.682  47.325    882
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 24.14 %
    Favored  : 73.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.30), residues: 782
  helix:  0.86 (0.27), residues: 366
  sheet: -1.69 (0.38), residues: 147
  loop : -1.42 (0.36), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1159 
 HIS   0.009   0.001   HIS B 387 
 PHE   0.010   0.001   PHE A1168 
 TYR   0.017   0.001   TYR A1214 
 ARG   0.002   0.000   ARG A1215 

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.7321 (p0) cc_final: 0.6156 (p0)
REVERT: A  413 HIS cc_start: 0.8109 (t-90) cc_final: 0.7876 (t-90)
REVERT: A 1094 ASP cc_start: 0.8162 (m-30) cc_final: 0.7904 (m-30)
REVERT: A 1157 MET cc_start: 0.7622 (tpp) cc_final: 0.6910 (tpp)
REVERT: B   92 VAL cc_start: 0.9183 (OUTLIER) cc_final: 0.8973 (p)
REVERT: B  110 MET cc_start: 0.8555 (mtp) cc_final: 0.8321 (mtt)
REVERT: B  125 GLN cc_start: 0.7715 (tp40) cc_final: 0.7418 (pt0)
  outliers start: 15
  outliers final: 10
  residues processed: 122
  average time/residue: 0.1677
  time to fit residues: 28.6078
Evaluate side-chains
  114 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue 1036 ILE
Chi-restraints excluded: chain A residue 1095 GLU
Chi-restraints excluded: chain A residue 1097 LEU
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  200 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 70 optimal weight:    0.4980
   chunk 39 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   chunk 59 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  98 ASN
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.119701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.095090 restraints weight = 14152.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.097955 restraints weight = 7779.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.099821 restraints weight = 5368.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.3357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6548  Z= 0.207
  Angle     :  0.631  12.753   8830  Z= 0.318
  Chirality :  0.044   0.247    959
  Planarity :  0.003   0.048   1140
  Dihedral  :  4.715  44.782    882
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 24.43 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.30), residues: 782
  helix:  0.69 (0.27), residues: 376
  sheet: -1.52 (0.40), residues: 136
  loop : -1.64 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1159 
 HIS   0.008   0.001   HIS B 387 
 PHE   0.011   0.001   PHE A1168 
 TYR   0.017   0.001   TYR A1214 
 ARG   0.002   0.000   ARG A1084 

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.7241 (p0) cc_final: 0.6141 (p0)
REVERT: A  413 HIS cc_start: 0.8066 (t-90) cc_final: 0.7839 (t-90)
REVERT: A 1094 ASP cc_start: 0.8124 (m-30) cc_final: 0.7876 (m-30)
REVERT: B   92 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.9023 (t)
REVERT: B  110 MET cc_start: 0.8477 (mtp) cc_final: 0.8275 (mtt)
REVERT: B  125 GLN cc_start: 0.7673 (tp40) cc_final: 0.7432 (pt0)
REVERT: B  142 PHE cc_start: 0.7438 (m-80) cc_final: 0.7201 (m-80)
  outliers start: 16
  outliers final: 11
  residues processed: 121
  average time/residue: 0.1659
  time to fit residues: 27.8289
Evaluate side-chains
  117 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue 1036 ILE
Chi-restraints excluded: chain A residue 1050 THR
Chi-restraints excluded: chain A residue 1095 GLU
Chi-restraints excluded: chain A residue 1097 LEU
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  114 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 5 optimal weight:    0.0770
   chunk 22 optimal weight:    0.2980
   chunk 32 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   chunk 59 optimal weight:    6.9990
   chunk 42 optimal weight:    0.6980
   chunk 1 optimal weight:    0.0170
   chunk 73 optimal weight:    0.8980
   chunk 58 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   overall best weight:    0.3376

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

Flipped N/Q/H residues before XYZ refinement:
A 491 HIS
B  98 ASN
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.122414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.098148 restraints weight = 14311.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.101020 restraints weight = 7836.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.103013 restraints weight = 5394.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.3690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6548  Z= 0.171
  Angle     :  0.632  13.102   8830  Z= 0.317
  Chirality :  0.044   0.348    959
  Planarity :  0.003   0.048   1140
  Dihedral  :  4.666  46.103    882
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 25.43 %
    Favored  : 72.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.30), residues: 782
  helix:  0.83 (0.27), residues: 369
  sheet: -1.58 (0.39), residues: 144
  loop : -1.35 (0.36), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1159 
 HIS   0.009   0.001   HIS B 387 
 PHE   0.010   0.001   PHE A1168 
 TYR   0.020   0.001   TYR A1214 
 ARG   0.002   0.000   ARG A1215 

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 0.748 
Fit side-chains
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.7266 (p0) cc_final: 0.6244 (p0)
REVERT: A  324 GLU cc_start: 0.7962 (pp20) cc_final: 0.7717 (pp20)
REVERT: A  413 HIS cc_start: 0.8069 (t-90) cc_final: 0.7807 (t-90)
REVERT: A  545 MET cc_start: 0.7041 (ppp) cc_final: 0.6837 (tpt)
REVERT: A 1094 ASP cc_start: 0.8142 (m-30) cc_final: 0.7898 (m-30)
REVERT: A 1157 MET cc_start: 0.7095 (tpp) cc_final: 0.6798 (ttm)
REVERT: B  125 GLN cc_start: 0.7597 (tp40) cc_final: 0.7394 (pt0)
REVERT: B  360 TYR cc_start: 0.7983 (m-80) cc_final: 0.7489 (m-10)
  outliers start: 12
  outliers final: 7
  residues processed: 132
  average time/residue: 0.1714
  time to fit residues: 31.0307
Evaluate side-chains
  114 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue 1095 GLU
Chi-restraints excluded: chain A residue 1097 LEU
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue  114 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0060
   chunk 14 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.7402

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

Flipped N/Q/H residues before XYZ refinement:
B  98 ASN
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.121025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.096383 restraints weight = 14519.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.099280 restraints weight = 8070.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.101196 restraints weight = 5595.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.3781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   6548  Z= 0.222
  Angle     :  0.682  13.387   8830  Z= 0.344
  Chirality :  0.045   0.349    959
  Planarity :  0.003   0.046   1140
  Dihedral  :  4.831  45.825    882
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 26.29 %
    Favored  : 72.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.29), residues: 782
  helix:  0.61 (0.27), residues: 375
  sheet: -1.49 (0.40), residues: 136
  loop : -1.46 (0.35), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1159 
 HIS   0.009   0.001   HIS B 387 
 PHE   0.027   0.001   PHE B 178 
 TYR   0.021   0.001   TYR A1241 
 ARG   0.003   0.000   ARG B 280 

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.725 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.7120 (p0) cc_final: 0.6291 (p0)
REVERT: A  413 HIS cc_start: 0.7996 (t-90) cc_final: 0.7726 (t-90)
REVERT: A 1094 ASP cc_start: 0.8146 (m-30) cc_final: 0.7888 (m-30)
REVERT: A 1157 MET cc_start: 0.7156 (tpp) cc_final: 0.6784 (ttm)
REVERT: B   98 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7843 (t160)
REVERT: B  360 TYR cc_start: 0.8017 (m-80) cc_final: 0.7559 (m-10)
  outliers start: 10
  outliers final: 9
  residues processed: 115
  average time/residue: 0.1689
  time to fit residues: 26.5631
Evaluate side-chains
  111 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  464 GLU
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue 1095 GLU
Chi-restraints excluded: chain A residue 1097 LEU
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain A residue 1232 VAL
Chi-restraints excluded: chain B residue   98 ASN
Chi-restraints excluded: chain B residue  114 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 3 optimal weight:    0.0060
   chunk 11 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 72 optimal weight:    0.0270
   chunk 67 optimal weight:    3.9990
   chunk 12 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 41 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.4454

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

Flipped N/Q/H residues before XYZ refinement:
B  98 ASN
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.121988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.097246 restraints weight = 14459.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.100198 restraints weight = 7917.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.102201 restraints weight = 5424.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.4007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   6548  Z= 0.195
  Angle     :  0.686  13.539   8830  Z= 0.344
  Chirality :  0.045   0.352    959
  Planarity :  0.003   0.046   1140
  Dihedral  :  4.780  45.970    882
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 25.43 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.29), residues: 782
  helix:  0.57 (0.27), residues: 375
  sheet: -1.41 (0.41), residues: 136
  loop : -1.44 (0.35), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1159 
 HIS   0.010   0.001   HIS B 387 
 PHE   0.021   0.001   PHE B 178 
 TYR   0.022   0.001   TYR A1214 
 ARG   0.002   0.000   ARG B 280 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2247.46 seconds
wall clock time: 41 minutes 12.71 seconds (2472.71 seconds total)